Name: rs6497292
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs6497292

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:28251049 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.246575 (65266/264690, TOPMED)
G=0.222558 (31183/140112, GnomAD)
G=0.12818 (4011/31292, ALFA) (+ 16 more)
G=0.42806 (12096/28258, 14KJPN)
G=0.42088 (7054/16760, 8.3KJPN)
G=0.3301 (2114/6404, 1000G_30x)
G=0.3279 (1642/5008, 1000G)
G=0.0566 (218/3854, ALSPAC)
G=0.0507 (188/3708, TWINSUK)
G=0.4099 (1201/2930, KOREAN)
G=0.3594 (639/1778, HapMap)
G=0.3644 (610/1674, Korea1K)
G=0.034 (34/998, GoNL)
G=0.083 (52/626, Chileans)
G=0.027 (16/600, NorthernSweden)
A=0.353 (94/266, SGDP_PRJ)
G=0.301 (65/216, Qatari)
G=0.440 (95/216, Vietnamese)
A=0.2 (2/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HERC2 : Intron Variant
Publications: 1 citation
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	31292	A=0.87182	G=0.12818
European	Sub	17512	A=0.93804	G=0.06196
African	Sub	3248	A=0.4440	G=0.5560
African Others	Sub	114	A=0.386	G=0.614
African American	Sub	3134	A=0.4461	G=0.5539
Asian	Sub	134	A=0.552	G=0.448
East Asian	Sub	104	A=0.558	G=0.442
Other Asian	Sub	30	A=0.53	G=0.47
Latin American 1	Sub	298	A=0.802	G=0.198
Latin American 2	Sub	6712	A=0.9027	G=0.0973
South Asian	Sub	114	A=0.763	G=0.237
Other	Sub	3274	A=0.9020	G=0.0980

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	A=0.753425	G=0.246575
gnomAD - Genomes	Global	Study-wide	140112	A=0.777442	G=0.222558
gnomAD - Genomes	European	Sub	75934	A=0.94665	G=0.05335
gnomAD - Genomes	African	Sub	41924	A=0.45017	G=0.54983
gnomAD - Genomes	American	Sub	13648	A=0.85881	G=0.14119
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.9058	G=0.0942
gnomAD - Genomes	East Asian	Sub	3128	A=0.5646	G=0.4354
gnomAD - Genomes	Other	Sub	2154	A=0.7776	G=0.2224
Allele Frequency Aggregator	Total	Global	31292	A=0.87182	G=0.12818
Allele Frequency Aggregator	European	Sub	17512	A=0.93804	G=0.06196
Allele Frequency Aggregator	Latin American 2	Sub	6712	A=0.9027	G=0.0973
Allele Frequency Aggregator	Other	Sub	3274	A=0.9020	G=0.0980
Allele Frequency Aggregator	African	Sub	3248	A=0.4440	G=0.5560
Allele Frequency Aggregator	Latin American 1	Sub	298	A=0.802	G=0.198
Allele Frequency Aggregator	Asian	Sub	134	A=0.552	G=0.448
Allele Frequency Aggregator	South Asian	Sub	114	A=0.763	G=0.237
14KJPN	JAPANESE	Study-wide	28258	A=0.57194	G=0.42806
8.3KJPN	JAPANESE	Study-wide	16760	A=0.57912	G=0.42088
1000Genomes_30x	Global	Study-wide	6404	A=0.6699	G=0.3301
1000Genomes_30x	African	Sub	1786	A=0.3600	G=0.6400
1000Genomes_30x	Europe	Sub	1266	A=0.9068	G=0.0932
1000Genomes_30x	South Asian	Sub	1202	A=0.7770	G=0.2230
1000Genomes_30x	East Asian	Sub	1170	A=0.6051	G=0.3949
1000Genomes_30x	American	Sub	980	A=0.874	G=0.126
1000Genomes	Global	Study-wide	5008	A=0.6721	G=0.3279
1000Genomes	African	Sub	1322	A=0.3616	G=0.6384
1000Genomes	East Asian	Sub	1008	A=0.6121	G=0.3879
1000Genomes	Europe	Sub	1006	A=0.9095	G=0.0905
1000Genomes	South Asian	Sub	978	A=0.770	G=0.230
1000Genomes	American	Sub	694	A=0.869	G=0.131
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9434	G=0.0566
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9493	G=0.0507
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5901	G=0.4099
HapMap	Global	Study-wide	1778	A=0.6406	G=0.3594
HapMap	American	Sub	768	A=0.740	G=0.260
HapMap	African	Sub	580	A=0.464	G=0.536
HapMap	Asian	Sub	254	A=0.618	G=0.382
HapMap	Europe	Sub	176	A=0.824	G=0.176
Korean Genome Project	KOREAN	Study-wide	1674	A=0.6356	G=0.3644
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.966	G=0.034
Chileans	Chilean	Study-wide	626	A=0.917	G=0.083
Northern Sweden	ACPOP	Study-wide	600	A=0.973	G=0.027
SGDP_PRJ	Global	Study-wide	266	A=0.353	G=0.647
Qatari	Global	Study-wide	216	A=0.699	G=0.301
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.560	G=0.440
Siberian	Global	Study-wide	8	A=0.2	G=0.8

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 15	NC_000015.10:g.28251049A>G
GRCh37.p13 chr 15	NC_000015.9:g.28496195A>G
HERC2 RefSeqGene	NG_016355.1:g.76101T>C
GRCh38.p14 chr 15 fix patch HG2139_PATCH	NW_011332701.1:g.384494A>G
GRCh38.p14 chr 15 alt locus HSCHR15_4_CTG8	NT_187660.1:g.498280A>G

Gene: HERC2, HECT and RLD domain containing E3 ubiquitin protein ligase 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HERC2 transcript	NM_004667.6:c.3051-2313T>C	N/A	Intron Variant
HERC2 transcript variant X5	XM_005268276.6:c.2937-231… XM_005268276.6:c.2937-2313T>C	N/A	Intron Variant
HERC2 transcript variant X1	XM_006720726.4:c.3051-231… XM_006720726.4:c.3051-2313T>C	N/A	Intron Variant
HERC2 transcript variant X6	XM_006720727.4:c.2793-231… XM_006720727.4:c.2793-2313T>C	N/A	Intron Variant
HERC2 transcript variant X3	XM_017022695.1:c.2937-231… XM_017022695.1:c.2937-2313T>C	N/A	Intron Variant
HERC2 transcript variant X4	XM_017022696.2:c.2937-231… XM_017022696.2:c.2937-2313T>C	N/A	Intron Variant
HERC2 transcript variant X2	XM_047433206.1:c.3024-231… XM_047433206.1:c.3024-2313T>C	N/A	Intron Variant
HERC2 transcript variant X7	XM_047433207.1:c.2568-231… XM_047433207.1:c.2568-2313T>C	N/A	Intron Variant
HERC2 transcript variant X8	XM_047433208.1:c.3051-231… XM_047433208.1:c.3051-2313T>C	N/A	Intron Variant
HERC2 transcript variant X9	XM_047433209.1:c.3051-231… XM_047433209.1:c.3051-2313T>C	N/A	Intron Variant
HERC2 transcript variant X10	XM_017022697.2:c.	N/A	Genic Upstream Transcript Variant
HERC2 transcript variant X11	XM_017022698.2:c.	N/A	Genic Upstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	A=	G
GRCh38.p14 chr 15	NC_000015.10:g.28251049=	NC_000015.10:g.28251049A>G
GRCh37.p13 chr 15	NC_000015.9:g.28496195=	NC_000015.9:g.28496195A>G
HERC2 RefSeqGene	NG_016355.1:g.76101=	NG_016355.1:g.76101T>C
GRCh38.p14 chr 15 fix patch HG2139_PATCH	NW_011332701.1:g.384494=	NW_011332701.1:g.384494A>G
GRCh38.p14 chr 15 alt locus HSCHR15_4_CTG8	NT_187660.1:g.498280=	NT_187660.1:g.498280A>G
HERC2 transcript	NM_004667.5:c.3051-2313=	NM_004667.5:c.3051-2313T>C
HERC2 transcript	NM_004667.6:c.3051-2313=	NM_004667.6:c.3051-2313T>C
HERC2 transcript variant X1	XM_005268275.1:c.3051-2313=	XM_005268275.1:c.3051-2313T>C
HERC2 transcript variant X2	XM_005268276.1:c.2937-2313=	XM_005268276.1:c.2937-2313T>C
HERC2 transcript variant X5	XM_005268276.6:c.2937-2313=	XM_005268276.6:c.2937-2313T>C
HERC2 transcript variant X3	XM_005268277.1:c.2937-2313=	XM_005268277.1:c.2937-2313T>C
HERC2 transcript variant X4	XM_005268278.1:c.2793-2313=	XM_005268278.1:c.2793-2313T>C
HERC2 transcript variant X5	XM_005268279.1:c.567-2313=	XM_005268279.1:c.567-2313T>C
HERC2 transcript variant X1	XM_006720726.4:c.3051-2313=	XM_006720726.4:c.3051-2313T>C
HERC2 transcript variant X6	XM_006720727.4:c.2793-2313=	XM_006720727.4:c.2793-2313T>C
HERC2 transcript variant X3	XM_017022695.1:c.2937-2313=	XM_017022695.1:c.2937-2313T>C
HERC2 transcript variant X4	XM_017022696.2:c.2937-2313=	XM_017022696.2:c.2937-2313T>C
HERC2 transcript variant X2	XM_047433206.1:c.3024-2313=	XM_047433206.1:c.3024-2313T>C
HERC2 transcript variant X7	XM_047433207.1:c.2568-2313=	XM_047433207.1:c.2568-2313T>C
HERC2 transcript variant X8	XM_047433208.1:c.3051-2313=	XM_047433208.1:c.3051-2313T>C
HERC2 transcript variant X9	XM_047433209.1:c.3051-2313=	XM_047433209.1:c.3051-2313T>C

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

63 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10784435	Jul 11, 2003 (116)
2	WI_SSAHASNP	ss12328102	Jul 11, 2003 (116)
3	PERLEGEN	ss23973190	Sep 20, 2004 (124)
4	ILLUMINA	ss65823306	Oct 14, 2006 (127)
5	AFFY	ss66241782	Nov 29, 2006 (127)
6	AFFY	ss76387460	Dec 06, 2007 (129)
7	KRIBB_YJKIM	ss82247994	Dec 15, 2007 (130)
8	HGSV	ss84232470	Dec 15, 2007 (130)
9	1000GENOMES	ss113955299	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss118172266	Feb 14, 2009 (130)
11	GMI	ss156361525	Dec 01, 2009 (131)
12	ILLUMINA	ss161050627	Dec 01, 2009 (131)
13	AFFY	ss173446253	Jul 04, 2010 (132)
14	BUSHMAN	ss200655818	Jul 04, 2010 (132)
15	1000GENOMES	ss226813677	Jul 14, 2010 (132)
16	1000GENOMES	ss236722860	Jul 15, 2010 (132)
17	1000GENOMES	ss243120787	Jul 15, 2010 (132)
18	GMI	ss282193255	May 04, 2012 (137)
19	PJP	ss291808406	May 09, 2011 (134)
20	ILLUMINA	ss479385898	Sep 08, 2015 (146)
21	TISHKOFF	ss564384238	Apr 25, 2013 (138)
22	SSMP	ss660096384	Apr 25, 2013 (138)
23	EVA-GONL	ss991625276	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1080004095	Aug 21, 2014 (142)
25	1000GENOMES	ss1352826718	Aug 21, 2014 (142)
26	DDI	ss1427576127	Apr 01, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1632673124	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1675667157	Apr 01, 2015 (144)
29	EVA_DECODE	ss1695637050	Apr 01, 2015 (144)
30	EVA_SVP	ss1713477707	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1808131814	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1935022788	Feb 12, 2016 (147)
33	JJLAB	ss2028291395	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2156688466	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2628638960	Nov 08, 2017 (151)
36	GRF	ss2701147693	Nov 08, 2017 (151)
37	GNOMAD	ss2933002999	Nov 08, 2017 (151)
38	SWEGEN	ss3013007950	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3027969921	Nov 08, 2017 (151)
40	ILLUMINA	ss3636288465	Oct 12, 2018 (152)
41	EVA_DECODE	ss3697586625	Jul 13, 2019 (153)
42	ACPOP	ss3740787964	Jul 13, 2019 (153)
43	EVA	ss3752892717	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3818209873	Jul 13, 2019 (153)
45	EVA	ss3834157123	Apr 27, 2020 (154)
46	SGDP_PRJ	ss3882554958	Apr 27, 2020 (154)
47	KRGDB	ss3931679447	Apr 27, 2020 (154)
48	KOGIC	ss3975854022	Apr 27, 2020 (154)
49	VINODS	ss4031999528	Apr 27, 2021 (155)
50	TOPMED	ss4985767148	Apr 27, 2021 (155)
51	TOMMO_GENOMICS	ss5215411587	Apr 27, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5297865419	Oct 16, 2022 (156)
53	EVA	ss5418203912	Oct 16, 2022 (156)
54	HUGCELL_USP	ss5491680180	Oct 16, 2022 (156)
55	EVA	ss5511383048	Oct 16, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5598979116	Oct 16, 2022 (156)
57	SANFORD_IMAGENETICS	ss5657178256	Oct 16, 2022 (156)
58	TOMMO_GENOMICS	ss5768988995	Oct 16, 2022 (156)
59	YY_MCH	ss5815189485	Oct 16, 2022 (156)
60	EVA	ss5827984950	Oct 16, 2022 (156)
61	EVA	ss5851228089	Oct 16, 2022 (156)
62	EVA	ss5875254834	Oct 16, 2022 (156)
63	EVA	ss5948588368	Oct 16, 2022 (156)
64	1000Genomes	NC_000015.9 - 28496195	Oct 12, 2018 (152)
65	1000Genomes_30x	NC_000015.10 - 28251049	Oct 16, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 28496195	Oct 12, 2018 (152)
67	Chileans	NC_000015.9 - 28496195	Apr 27, 2020 (154)
68	gnomAD - Genomes	NC_000015.10 - 28251049	Apr 27, 2021 (155)
69	Genome of the Netherlands Release 5	NC_000015.9 - 28496195	Apr 27, 2020 (154)
70	HapMap	NC_000015.10 - 28251049	Apr 27, 2020 (154)
71	KOREAN population from KRGDB	NC_000015.9 - 28496195	Apr 27, 2020 (154)
72	Korean Genome Project	NC_000015.10 - 28251049	Apr 27, 2020 (154)
73	Northern Sweden	NC_000015.9 - 28496195	Jul 13, 2019 (153)
74	Qatari	NC_000015.9 - 28496195	Apr 27, 2020 (154)
75	SGDP_PRJ	NC_000015.9 - 28496195	Apr 27, 2020 (154)
76	Siberian	NC_000015.9 - 28496195	Apr 27, 2020 (154)
77	8.3KJPN	NC_000015.9 - 28496195	Apr 27, 2021 (155)
78	14KJPN	NC_000015.10 - 28251049	Oct 16, 2022 (156)
79	TopMed	NC_000015.10 - 28251049	Apr 27, 2021 (155)
80	UK 10K study - Twins	NC_000015.9 - 28496195	Oct 12, 2018 (152)
81	A Vietnamese Genetic Variation Database	NC_000015.9 - 28496195	Jul 13, 2019 (153)
82	ALFA	NC_000015.10 - 28251049	Apr 27, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs16950937	Dec 02, 2004 (124)
rs59828374	May 25, 2008 (130)
rs60047725	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66241782, ss76387460, ss84232470, ss113955299, ss118172266, ss173446253, ss200655818, ss282193255, ss291808406, ss1695637050, ss1713477707	NC_000015.8:26169789:A:G	NC_000015.10:28251048:A:G	(self)
65874063, 36577429, 148870, 16339158, 38856841, 14072829, 17064718, 34571938, 9204820, 73380894, 36577429, 8138390, ss226813677, ss236722860, ss243120787, ss479385898, ss564384238, ss660096384, ss991625276, ss1080004095, ss1352826718, ss1427576127, ss1632673124, ss1675667157, ss1808131814, ss1935022788, ss2028291395, ss2156688466, ss2628638960, ss2701147693, ss2933002999, ss3013007950, ss3636288465, ss3740787964, ss3752892717, ss3834157123, ss3882554958, ss3931679447, ss5215411587, ss5418203912, ss5511383048, ss5657178256, ss5827984950, ss5948588368	NC_000015.9:28496194:A:G	NC_000015.10:28251048:A:G	(self)
86505051, 464316187, 1232762, 32232023, 102826099, 201312808, 6562104688, ss3027969921, ss3697586625, ss3818209873, ss3975854022, ss4985767148, ss5297865419, ss5491680180, ss5598979116, ss5768988995, ss5815189485, ss5851228089, ss5875254834	NC_000015.10:28251048:A:G	NC_000015.10:28251048:A:G	(self)
ss10784435, ss12328102	NT_010280.15:855452:A:G	NC_000015.10:28251048:A:G	(self)
ss23973190, ss65823306, ss82247994, ss156361525, ss161050627	NT_026446.14:4931341:A:G	NC_000015.10:28251048:A:G	(self)
ss4031999528	NT_187660.1:498279:A:G	NC_000015.10:28251048:A:G	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs6497292

PMID	Title	Author	Year	Journal
18252221	Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene.	Kayser M et al.	2008	American journal of human genetics

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs6497292