Name: rs10399749
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.

rs10399749

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:55299 (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: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.33178 (9242/27856, 14KJPN)
T=0.33404 (5515/16510, 8.3KJPN)
T=0.0492 (378/7688, ALFA) (+ 10 more)
T=0.3381 (2165/6404, 1000G_30x)
T=0.3538 (1019/2880, KOREAN)
T=0.3624 (653/1802, Korea1K)
T=0.171 (171/998, GoNL)
T=0.310 (139/448, NorthernSweden)
T=0.000 (0/314, HapMap)
C=0.399 (95/238, SGDP_PRJ)
T=0.274 (46/168, Qatari)
T=0.30 (9/30, GENOME_DK)
C=0.33 (4/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
Publications: 0 citations
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	7688	C=0.9508	A=0.0000, T=0.0492
European	Sub	5654	C=0.9759	A=0.0000, T=0.0241
African	Sub	1218	C=0.8013	A=0.0000, T=0.1987
African Others	Sub	46	C=0.78	A=0.00, T=0.22
African American	Sub	1172	C=0.8020	A=0.0000, T=0.1980
Asian	Sub	38	C=1.00	A=0.00, T=0.00
East Asian	Sub	28	C=1.00	A=0.00, T=0.00
Other Asian	Sub	10	C=1.0	A=0.0, T=0.0
Latin American 1	Sub	100	C=1.00	A=0.00, T=0.00
Latin American 2	Sub	346	C=1.000	A=0.000, T=0.000
South Asian	Sub	66	C=1.00	A=0.00, T=0.00
Other	Sub	266	C=1.000	A=0.000, T=0.000

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
14KJPN	JAPANESE	Study-wide	27856	C=0.66822	T=0.33178
8.3KJPN	JAPANESE	Study-wide	16510	C=0.66596	T=0.33404
Allele Frequency Aggregator	Total	Global	7688	C=0.9508	A=0.0000, T=0.0492
Allele Frequency Aggregator	European	Sub	5654	C=0.9759	A=0.0000, T=0.0241
Allele Frequency Aggregator	African	Sub	1218	C=0.8013	A=0.0000, T=0.1987
Allele Frequency Aggregator	Latin American 2	Sub	346	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	266	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	100	C=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	66	C=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	38	C=1.00	A=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.6619	T=0.3381
1000Genomes_30x	African	Sub	1786	C=0.5476	T=0.4524
1000Genomes_30x	Europe	Sub	1266	C=0.7915	T=0.2085
1000Genomes_30x	South Asian	Sub	1202	C=0.7121	T=0.2879
1000Genomes_30x	East Asian	Sub	1170	C=0.6410	T=0.3590
1000Genomes_30x	American	Sub	980	C=0.666	T=0.334
KOREAN population from KRGDB	KOREAN	Study-wide	2880	C=0.6462	T=0.3538
Korean Genome Project	KOREAN	Study-wide	1802	C=0.6376	T=0.3624
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.829	T=0.171
Northern Sweden	ACPOP	Study-wide	448	C=0.690	T=0.310
HapMap	Global	Study-wide	314	C=1.000	T=0.000
HapMap	American	Sub	114	C=1.000	T=0.000
HapMap	African	Sub	112	C=1.000	T=0.000
HapMap	Asian	Sub	88	C=1.00	T=0.00
SGDP_PRJ	Global	Study-wide	238	C=0.399	T=0.601
Qatari	Global	Study-wide	168	C=0.726	T=0.274
The Danish reference pan genome	Danish	Study-wide	30	C=0.70	T=0.30
Siberian	Global	Study-wide	12	C=0.33	T=0.67

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 1	NC_000001.11:g.55299C>A
GRCh38.p14 chr 1	NC_000001.11:g.55299C>T
GRCh37.p13 chr 1	NC_000001.10:g.55299C>A
GRCh37.p13 chr 1	NC_000001.10:g.55299C>T

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	C=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.55299=	NC_000001.11:g.55299C>A	NC_000001.11:g.55299C>T
GRCh37.p13 chr 1	NC_000001.10:g.55299=	NC_000001.10:g.55299C>A	NC_000001.10:g.55299C>T

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#.

34 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss14687333	Dec 05, 2003 (119)
2	CSHL-HAPMAP	ss16401979	Feb 27, 2004 (120)
3	ILLUMINA-UK	ss118438121	Feb 14, 2009 (130)
4	GMI	ss154521915	Dec 01, 2009 (131)
5	1000GENOMES	ss218190319	Jul 14, 2010 (132)
6	1000GENOMES	ss230395378	Jul 14, 2010 (132)
7	1000GENOMES	ss238114927	Jul 15, 2010 (132)
8	GMI	ss275679902	May 04, 2012 (137)
9	SSMP	ss647514821	Apr 25, 2013 (138)
10	EVA-GONL	ss974768743	Aug 21, 2014 (142)
11	DDI	ss1425684544	Apr 01, 2015 (144)
12	EVA_GENOME_DK	ss1573850712	Apr 01, 2015 (144)
13	HAMMER_LAB	ss1793705023	Sep 08, 2015 (146)
14	WEILL_CORNELL_DGM	ss1917958223	Feb 12, 2016 (147)
15	GENOMED	ss1966667266	Jul 19, 2016 (147)
16	USC_VALOUEV	ss2147483701	Dec 20, 2016 (150)
17	GRF	ss2697372977	Nov 08, 2017 (151)
18	GNOMAD	ss2750603671	Nov 08, 2017 (151)
19	SWEGEN	ss2986141909	Nov 08, 2017 (151)
20	EVA_DECODE	ss3685990385	Jul 12, 2019 (153)
21	ACPOP	ss3726715181	Jul 12, 2019 (153)
22	EVA	ss3745720524	Jul 12, 2019 (153)
23	EVA	ss3825981326	Apr 25, 2020 (154)
24	SGDP_PRJ	ss3847983921	Apr 25, 2020 (154)
25	KRGDB	ss3892823768	Apr 25, 2020 (154)
26	KOGIC	ss3943622540	Apr 25, 2020 (154)
27	TOMMO_GENOMICS	ss5142032637	Apr 25, 2021 (155)
28	1000G_HIGH_COVERAGE	ss5512474910	Oct 12, 2022 (156)
29	SANFORD_IMAGENETICS	ss5624742460	Oct 12, 2022 (156)
30	TOMMO_GENOMICS	ss5666165130	Oct 12, 2022 (156)
31	YY_MCH	ss5800240469	Oct 12, 2022 (156)
32	EVA	ss5831416613	Oct 12, 2022 (156)
33	EVA	ss5906703791	Oct 12, 2022 (156)
34	EVA	ss5936581778	Oct 12, 2022 (156)
35	1000Genomes_30x	NC_000001.11 - 55299	Oct 12, 2022 (156)
36	The Danish reference pan genome	NC_000001.10 - 55299	Apr 25, 2020 (154)
37	gnomAD - Genomes Submission ignored due to conflicting rows: Row 3944 (NC_000001.11:55298:C:A 1/101532) Row 3945 (NC_000001.11:55298:C:T 32371/100838)	-	Apr 25, 2021 (155)
38	gnomAD - Genomes Submission ignored due to conflicting rows: Row 3944 (NC_000001.11:55298:C:A 1/101532) Row 3945 (NC_000001.11:55298:C:T 32371/100838)	-	Apr 25, 2021 (155)
39	Genome of the Netherlands Release 5	NC_000001.10 - 55299	Apr 25, 2020 (154)
40	HapMap	NC_000001.11 - 55299	Apr 25, 2020 (154)
41	KOREAN population from KRGDB	NC_000001.10 - 55299	Apr 25, 2020 (154)
42	Korean Genome Project	NC_000001.11 - 55299	Apr 25, 2020 (154)
43	Northern Sweden	NC_000001.10 - 55299	Jul 12, 2019 (153)
44	Qatari	NC_000001.10 - 55299	Apr 25, 2020 (154)
45	SGDP_PRJ	NC_000001.10 - 55299	Apr 25, 2020 (154)
46	Siberian	NC_000001.10 - 55299	Apr 25, 2020 (154)
47	8.3KJPN	NC_000001.10 - 55299	Apr 25, 2021 (155)
48	14KJPN	NC_000001.11 - 55299	Oct 12, 2022 (156)
49	ALFA	NC_000001.11 - 55299	Apr 25, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
4928180230	NC_000001.11:55298:C:A	NC_000001.11:55298:C:A	(self)
ss118438121, ss275679902	NC_000001.9:45161:C:T	NC_000001.11:55298:C:T	(self)
1357946, 9, 1162, 46, 153, 901, 55, 1944, ss218190319, ss230395378, ss238114927, ss647514821, ss974768743, ss1425684544, ss1573850712, ss1793705023, ss1917958223, ss1966667266, ss2147483701, ss2697372977, ss2750603671, ss2986141909, ss3726715181, ss3745720524, ss3825981326, ss3847983921, ss3892823768, ss5142032637, ss5624742460, ss5831416613, ss5936581778	NC_000001.10:55298:C:T	NC_000001.11:55298:C:T	(self)
845, 1, 541, 2234, 4928180230, ss3685990385, ss3943622540, ss5512474910, ss5666165130, ss5800240469, ss5906703791	NC_000001.11:55298:C:T	NC_000001.11:55298:C:T	(self)
ss14687333, ss16401979	NT_077402.1:45161:C:T	NC_000001.11:55298:C:T	(self)
ss154521915	NT_077402.2:45298:C:T	NC_000001.11:55298:C:T	(self)

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

No publications for rs10399749

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs10399749