Name: rs5949028
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.

rs5949028

Current Build 156

Released September 21, 2022

Organism

Homo sapiens

Position

chrY:1636773 (GRCh38.p14)

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.

This SNP has mapping conflicts. See here for details.

Alleles

C>A / C>T

Variation Type

SNV Single Nucleotide Variation

Frequency

T=0.408451 (108113/264690, TOPMED)

T=0.411848 (57667/140020, GnomAD)

T=0.38242 (15085/39446, ALFA) (+ 8 more)

C=0.29167 (8242/28258, 14KJPN)

C=0.29117 (4880/16760, 8.3KJPN)

T=0.4608 (2214/4805, 1000G_30x)

T=0.4710 (1778/3775, 1000G)

T=0.004 (2/534, MGP)

C=0.300 (122/406, SGDP_PRJ)

T=0.407 (44/108, Qatari)

C=0.19 (6/32, Vietnamese)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ASMT : Intron Variant
Publications: 2 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	39446	C=0.61758	A=0.00000, T=0.38242
European	Sub	31588	C=0.62100	A=0.00000, T=0.37900
African	Sub	3286	C=0.6178	A=0.0000, T=0.3822
African Others	Sub	116	C=0.647	A=0.000, T=0.353
African American	Sub	3170	C=0.6167	A=0.0000, T=0.3833
Asian	Sub	430	C=0.300	A=0.000, T=0.700
East Asian	Sub	368	C=0.285	A=0.000, T=0.715
Other Asian	Sub	62	C=0.39	A=0.00, T=0.61
Latin American 1	Sub	196	C=0.643	A=0.000, T=0.357
Latin American 2	Sub	826	C=0.599	A=0.000, T=0.401
South Asian	Sub	132	C=0.667	A=0.000, T=0.333
Other	Sub	2988	C=0.6282	A=0.0000, T=0.3718

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	C=0.591549	T=0.408451
gnomAD - Genomes	Global	Study-wide	140020	C=0.588152	T=0.411848
gnomAD - Genomes	European	Sub	75800	C=0.60141	T=0.39859
gnomAD - Genomes	African	Sub	41994	C=0.59187	T=0.40813
gnomAD - Genomes	American	Sub	13630	C=0.57828	T=0.42172
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.5461	T=0.4539
gnomAD - Genomes	East Asian	Sub	3128	C=0.3159	T=0.6841
gnomAD - Genomes	Other	Sub	2148	C=0.5717	T=0.4283
Allele Frequency Aggregator	Total	Global	39446	C=0.61758	A=0.00000, T=0.38242
Allele Frequency Aggregator	European	Sub	31588	C=0.62100	A=0.00000, T=0.37900
Allele Frequency Aggregator	African	Sub	3286	C=0.6178	A=0.0000, T=0.3822
Allele Frequency Aggregator	Other	Sub	2988	C=0.6282	A=0.0000, T=0.3718
Allele Frequency Aggregator	Latin American 2	Sub	826	C=0.599	A=0.000, T=0.401
Allele Frequency Aggregator	Asian	Sub	430	C=0.300	A=0.000, T=0.700
Allele Frequency Aggregator	Latin American 1	Sub	196	C=0.643	A=0.000, T=0.357
Allele Frequency Aggregator	South Asian	Sub	132	C=0.667	A=0.000, T=0.333
14KJPN	JAPANESE	Study-wide	28258	C=0.29167	T=0.70833
8.3KJPN	JAPANESE	Study-wide	16760	C=0.29117	T=0.70883
1000Genomes_30x	Global	Study-wide	4805	C=0.5392	T=0.4608
1000Genomes_30x	African	Sub	1328	C=0.5648	T=0.4352
1000Genomes_30x	Europe	Sub	961	C=0.579	T=0.421
1000Genomes_30x	South Asian	Sub	883	C=0.607	T=0.393
1000Genomes_30x	East Asian	Sub	878	C=0.311	T=0.689
1000Genomes_30x	American	Sub	755	C=0.630	T=0.370
1000Genomes	Global	Study-wide	3775	C=0.5290	T=0.4710
1000Genomes	African	Sub	1003	C=0.5583	T=0.4417
1000Genomes	Europe	Sub	766	C=0.572	T=0.428
1000Genomes	East Asian	Sub	764	C=0.302	T=0.698
1000Genomes	South Asian	Sub	718	C=0.613	T=0.387
1000Genomes	American	Sub	524	C=0.626	T=0.374
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.996	T=0.004
SGDP_PRJ	Global	Study-wide	406	C=0.300	T=0.700
Qatari	Global	Study-wide	108	C=0.593	T=0.407
A Vietnamese Genetic Variation Database	Global	Study-wide	32	C=0.19	T=0.81

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 Y	NC_000024.10:g.1636773C>A
GRCh38.p14 chr Y	NC_000024.10:g.1636773C>T
GRCh37.p13 chr Y	NC_000024.9:g.1705666C>A
GRCh37.p13 chr Y	NC_000024.9:g.1705666C>T
ASMT RefSeqGene	NG_016337.1:g.46319C>A
ASMT RefSeqGene	NG_016337.1:g.46319C>T
GRCh38.p14 chr X	NC_000023.11:g.1636773C>A
GRCh38.p14 chr X	NC_000023.11:g.1636773C>T
GRCh37.p13 chr X	NC_000023.10:g.1755666C>A
GRCh37.p13 chr X	NC_000023.10:g.1755666C>T

Gene: ASMT, acetylserotonin O-methyltransferase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ASMT transcript variant 1	NM_001171038.2:c.910+213C… NM_001171038.2:c.910+213C>A	N/A	Intron Variant
ASMT transcript variant 3	NM_001171039.1:c.685+213C… NM_001171039.1:c.685+213C>A	N/A	Intron Variant
ASMT transcript variant 2	NM_004043.3:c.910+213C>A	N/A	Intron 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	C=	A	T
GRCh38.p14 chr Y	NC_000024.10:g.1636773=	NC_000024.10:g.1636773C>A	NC_000024.10:g.1636773C>T
GRCh37.p13 chr Y	NC_000024.9:g.1705666=	NC_000024.9:g.1705666C>A	NC_000024.9:g.1705666C>T
ASMT RefSeqGene	NG_016337.1:g.46319=	NG_016337.1:g.46319C>A	NG_016337.1:g.46319C>T
GRCh38.p14 chr X	NC_000023.11:g.1636773=	NC_000023.11:g.1636773C>A	NC_000023.11:g.1636773C>T
GRCh37.p13 chr X	NC_000023.10:g.1755666=	NC_000023.10:g.1755666C>A	NC_000023.10:g.1755666C>T
ASMT transcript variant 1	NM_001171038.1:c.910+213=	NM_001171038.1:c.910+213C>A	NM_001171038.1:c.910+213C>T
ASMT transcript variant 1	NM_001171038.2:c.910+213=	NM_001171038.2:c.910+213C>A	NM_001171038.2:c.910+213C>T
ASMT transcript variant 3	NM_001171039.1:c.685+213=	NM_001171039.1:c.685+213C>A	NM_001171039.1:c.685+213C>T
ASMT transcript variant 2	NM_004043.2:c.910+213=	NM_004043.2:c.910+213C>A	NM_004043.2:c.910+213C>T
ASMT transcript variant 2	NM_004043.3:c.910+213=	NM_004043.3:c.910+213C>A	NM_004043.3:c.910+213C>T
ASMT transcript variant X1	XM_005274433.1:c.826+213=	XM_005274433.1:c.826+213C>A	XM_005274433.1:c.826+213C>T
ASMT transcript variant X2	XM_005274782.1:c.826+213=	XM_005274782.1:c.826+213C>A	XM_005274782.1:c.826+213C>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#.

58 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8548456	Sep 28, 2016 (149)
2	HGSV	ss83868720	Dec 15, 2007 (130)
3	ILLUMINA-UK	ss115585216	Feb 14, 2009 (131)
4	ENSEMBL	ss144456492	Dec 01, 2009 (131)
5	ILLUMINA	ss160752119	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss162997525	Jul 04, 2010 (132)
7	COMPLETE_GENOMICS	ss164293837	Jul 04, 2010 (132)
8	COMPLETE_GENOMICS	ss166019633	Jul 04, 2010 (132)
9	ILLUMINA	ss244303865	Jul 04, 2010 (132)
10	1000GENOMES	ss341260109	May 09, 2011 (137)
11	ILLUMINA	ss482186194	Jul 19, 2016 (147)
12	ILLUMINA	ss482803448	May 04, 2012 (137)
13	ILLUMINA	ss484352364	May 04, 2012 (137)
14	ILLUMINA	ss534779876	Jul 19, 2016 (147)
15	SSMP	ss662666286	Apr 25, 2013 (138)
16	WARNICH_LAB	ss678451371	Apr 25, 2013 (138)
17	ILLUMINA	ss779135690	Sep 08, 2015 (146)
18	ILLUMINA	ss781882911	Jul 19, 2016 (147)
19	ILLUMINA	ss834600321	Jul 19, 2016 (147)
20	JMKIDD_LAB	ss1082755740	Aug 21, 2014 (142)
21	1000GENOMES	ss1553293862	Apr 01, 2015 (144)
22	EVA_MGP	ss1711576335	Apr 01, 2015 (144)
23	WEILL_CORNELL_DGM	ss1939084574	Feb 12, 2016 (147)
24	ILLUMINA	ss1958164056	Feb 12, 2016 (147)
25	TMC_SNPDB	ss1997226593	Jul 19, 2016 (147)
26	SYSTEMSBIOZJU	ss2629652045	Nov 08, 2017 (151)
27	ILLUMINA	ss2634933271	Nov 08, 2017 (151)
28	GNOMAD	ss2975946470	Nov 08, 2017 (151)
29	AFFY	ss2986140726	Nov 08, 2017 (151)
30	SWEGEN	ss3019544727	Nov 08, 2017 (151)
31	ILLUMINA	ss3022984202	Nov 08, 2017 (151)
32	BIOINF_KMB_FNS_UNIBA	ss3028992677	Nov 08, 2017 (151)
33	ILLUMINA	ss3630387176	Oct 12, 2018 (152)
34	ILLUMINA	ss3632820718	Oct 12, 2018 (152)
35	ILLUMINA	ss3637013408	Oct 12, 2018 (152)
36	OMUKHERJEE_ADBS	ss3646570502	Oct 12, 2018 (152)
37	OMUKHERJEE_ADBS	ss3646577357	Oct 12, 2018 (152)
38	ILLUMINA	ss3653541969	Oct 12, 2018 (152)
39	EVA	ss3769854816	Jul 14, 2019 (153)
40	PACBIO	ss3788865353	Jul 14, 2019 (153)
41	PACBIO	ss3793727371	Jul 14, 2019 (153)
42	PACBIO	ss3798612871	Jul 14, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3822711310	Jul 14, 2019 (153)
44	EVA	ss3836066234	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3890881239	Apr 27, 2020 (154)
46	GNOMAD	ss4367077489	Apr 26, 2021 (155)
47	TOPMED	ss5113787054	Apr 26, 2021 (155)
48	TOMMO_GENOMICS	ss5233313406	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5311614647	Oct 17, 2022 (156)
50	EVA	ss5316068701	Oct 17, 2022 (156)
51	HUGCELL_USP	ss5503386616	Oct 17, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5619365932	Oct 17, 2022 (156)
53	SANFORD_IMAGENETICS	ss5664779583	Oct 17, 2022 (156)
54	TOMMO_GENOMICS	ss5794672895	Oct 17, 2022 (156)
55	YY_MCH	ss5818842422	Oct 17, 2022 (156)
56	EVA	ss5856992822	Oct 17, 2022 (156)
57	EVA	ss5897816737	Oct 17, 2022 (156)
58	EVA	ss5977726924	Oct 17, 2022 (156)
59	1000Genomes	NC_000023.10 - 1755666	Oct 12, 2018 (152)
60	1000Genomes_30x	NC_000023.11 - 1636773	Oct 17, 2022 (156)
61	gnomAD - Genomes	NC_000023.11 - 1636773	Apr 26, 2021 (155)
62	Medical Genome Project healthy controls from Spanish population	NC_000023.10 - 1755666	Apr 27, 2020 (154)
63	Qatari	NC_000023.10 - 1755666	Apr 27, 2020 (154)
64	SGDP_PRJ	NC_000023.10 - 1755666	Apr 27, 2020 (154)
65	8.3KJPN	NC_000023.10 - 1755666	Apr 26, 2021 (155)
66	14KJPN	NC_000023.11 - 1636773	Oct 17, 2022 (156)
67	TopMed	NC_000023.11 - 1636773	Apr 26, 2021 (155)
68	A Vietnamese Genetic Variation Database	NC_000023.10 - 1755666	Jul 14, 2019 (153)
69	ALFA	NC_000024.10 - 1636773	Apr 26, 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)
rs6644788	Aug 26, 2003 (117)
rs60060276	May 25, 2008 (130)
rs73620124	Dec 02, 2009 (131)
rs146453995	May 04, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10306228353	NC_000024.10:1636772:C:A	NC_000024.10:1636772:C:A	(self)
ss83868720	NC_000023.8:1799492:C:T	NC_000024.10:1636772:C:T	(self)
ss115585216, ss162997525, ss164293837, ss166019633, ss484352364	NC_000023.9:1715665:C:T	NC_000024.10:1636772:C:T	(self)
81280748, 692095, 21126496, 42898219, 91282713, 9911890, ss341260109, ss662666286, ss678451371, ss779135690, ss1082755740, ss1553293862, ss1711576335, ss1939084574, ss1958164056, ss1997226593, ss2629652045, ss2634933271, ss2975946470, ss3019544727, ss3022984202, ss3630387176, ss3632820718, ss3646570502, ss3653541969, ss3769854816, ss3788865353, ss3793727371, ss3798612871, ss3836066234, ss3890881239, ss5233313406, ss5316068701, ss5664779583, ss5977726924	NC_000023.10:1755665:C:T	NC_000024.10:1636772:C:T	(self)
106891867, 573886429, 128509999, 677393411, ss3028992677, ss3822711310, ss4367077489, ss5113787054, ss5311614647, ss5503386616, ss5619365932, ss5794672895, ss5818842422, ss5856992822, ss5897816737	NC_000023.11:1636772:C:T	NC_000024.10:1636772:C:T	(self)
ss482186194, ss482803448, ss534779876, ss781882911, ss834600321, ss2986140726, ss3637013408, ss3646577357	NC_000024.9:1705665:C:T	NC_000024.10:1636772:C:T	(self)
10306228353	NC_000024.10:1636772:C:T	NC_000024.10:1636772:C:T	(self)
ss8548456	NT_033330.5:257710:C:T	NC_000024.10:1636772:C:T	(self)
ss144456492, ss160752119, ss244303865	NT_167204.1:441431:C:T	NC_000024.10:1636772:C:T	(self)

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

2 citations for rs5949028

PMID	Title	Author	Year	Journal
20442744	Linkage and candidate gene studies of autism spectrum disorders in European populations.	Holt R et al.	2010	European journal of human genetics
23995775	Association between ASMT and autistic-like traits in children from a Swedish nationwide cohort.	Jonsson L et al.	2014	Psychiatric 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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs5949028