Name: rs813992
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.

rs813992

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:148681817 (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: T>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.277876 (73551/264690, TOPMED)
T=0.278554 (38978/139930, GnomAD)
T=0.08429 (2382/28258, 14KJPN) (+ 18 more)
T=0.26070 (5506/21120, ALFA)
T=0.08419 (1411/16760, 8.3KJPN)
T=0.2856 (1829/6404, 1000G_30x)
T=0.2790 (1397/5008, 1000G)
T=0.2458 (1101/4480, Estonian)
T=0.2089 (805/3854, ALSPAC)
T=0.2082 (772/3708, TWINSUK)
T=0.0679 (199/2930, KOREAN)
T=0.3171 (600/1892, HapMap)
T=0.0606 (111/1832, Korea1K)
T=0.179 (179/998, GoNL)
T=0.188 (113/600, NorthernSweden)
T=0.156 (80/514, SGDP_PRJ)
T=0.375 (81/216, Qatari)
T=0.060 (13/216, Vietnamese)
T=0.13 (7/54, Siberian)
T=0.17 (7/40, GENOME_DK)
T=0.17 (4/24, Ancient Sardinia)

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	21120	T=0.26070	A=0.00000, C=0.73930
European	Sub	15346	T=0.21230	A=0.00000, C=0.78770
African	Sub	3706	T=0.4927	A=0.0000, C=0.5073
African Others	Sub	134	T=0.627	A=0.000, C=0.373
African American	Sub	3572	T=0.4877	A=0.0000, C=0.5123
Asian	Sub	124	T=0.065	A=0.000, C=0.935
East Asian	Sub	96	T=0.08	A=0.00, C=0.92
Other Asian	Sub	28	T=0.00	A=0.00, C=1.00
Latin American 1	Sub	168	T=0.262	A=0.000, C=0.738
Latin American 2	Sub	670	T=0.158	A=0.000, C=0.842
South Asian	Sub	98	T=0.36	A=0.00, C=0.64
Other	Sub	1008	T=0.2272	A=0.0000, C=0.7728

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.277876	C=0.722124
gnomAD - Genomes	Global	Study-wide	139930	T=0.278554	C=0.721446
gnomAD - Genomes	European	Sub	75834	T=0.20271	C=0.79729
gnomAD - Genomes	African	Sub	41898	T=0.47542	C=0.52458
gnomAD - Genomes	American	Sub	13596	T=0.17446	C=0.82554
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.1650	C=0.8350
gnomAD - Genomes	East Asian	Sub	3130	T=0.0725	C=0.9275
gnomAD - Genomes	Other	Sub	2150	T=0.2512	C=0.7488
14KJPN	JAPANESE	Study-wide	28258	T=0.08429	C=0.91571
Allele Frequency Aggregator	Total	Global	21120	T=0.26070	A=0.00000, C=0.73930
Allele Frequency Aggregator	European	Sub	15346	T=0.21230	A=0.00000, C=0.78770
Allele Frequency Aggregator	African	Sub	3706	T=0.4927	A=0.0000, C=0.5073
Allele Frequency Aggregator	Other	Sub	1008	T=0.2272	A=0.0000, C=0.7728
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.158	A=0.000, C=0.842
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.262	A=0.000, C=0.738
Allele Frequency Aggregator	Asian	Sub	124	T=0.065	A=0.000, C=0.935
Allele Frequency Aggregator	South Asian	Sub	98	T=0.36	A=0.00, C=0.64
8.3KJPN	JAPANESE	Study-wide	16760	T=0.08419	C=0.91581
1000Genomes_30x	Global	Study-wide	6404	T=0.2856	C=0.7144
1000Genomes_30x	African	Sub	1786	T=0.5297	C=0.4703
1000Genomes_30x	Europe	Sub	1266	T=0.2046	C=0.7954
1000Genomes_30x	South Asian	Sub	1202	T=0.3228	C=0.6772
1000Genomes_30x	East Asian	Sub	1170	T=0.0675	C=0.9325
1000Genomes_30x	American	Sub	980	T=0.160	C=0.840
1000Genomes	Global	Study-wide	5008	T=0.2790	C=0.7210
1000Genomes	African	Sub	1322	T=0.5303	C=0.4697
1000Genomes	East Asian	Sub	1008	T=0.0675	C=0.9325
1000Genomes	Europe	Sub	1006	T=0.1958	C=0.8042
1000Genomes	South Asian	Sub	978	T=0.325	C=0.675
1000Genomes	American	Sub	694	T=0.163	C=0.837
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.2458	C=0.7542
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.2089	C=0.7911
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.2082	C=0.7918
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0679	A=0.0000, C=0.9321, G=0.0000
HapMap	Global	Study-wide	1892	T=0.3171	C=0.6829
HapMap	American	Sub	770	T=0.248	C=0.752
HapMap	African	Sub	692	T=0.520	C=0.480
HapMap	Asian	Sub	254	T=0.059	C=0.941
HapMap	Europe	Sub	176	T=0.193	C=0.807
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0606	C=0.9394
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.179	C=0.821
Northern Sweden	ACPOP	Study-wide	600	T=0.188	C=0.812
SGDP_PRJ	Global	Study-wide	514	T=0.156	C=0.844
Qatari	Global	Study-wide	216	T=0.375	C=0.625
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.060	C=0.940
Siberian	Global	Study-wide	54	T=0.13	C=0.87
The Danish reference pan genome	Danish	Study-wide	40	T=0.17	C=0.82
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	24	T=0.17	C=0.83

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 3	NC_000003.12:g.148681817T>A
GRCh38.p14 chr 3	NC_000003.12:g.148681817T>C
GRCh38.p14 chr 3	NC_000003.12:g.148681817T>G
GRCh37.p13 chr 3	NC_000003.11:g.148399604T>A
GRCh37.p13 chr 3	NC_000003.11:g.148399604T>C
GRCh37.p13 chr 3	NC_000003.11:g.148399604T>G

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	T=	A	C	G
GRCh38.p14 chr 3	NC_000003.12:g.148681817=	NC_000003.12:g.148681817T>A	NC_000003.12:g.148681817T>C	NC_000003.12:g.148681817T>G
GRCh37.p13 chr 3	NC_000003.11:g.148399604=	NC_000003.11:g.148399604T>A	NC_000003.11:g.148399604T>C	NC_000003.11:g.148399604T>G

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#.

87 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1067858	Oct 05, 2000 (86)
2	KWOK	ss1981575	Oct 18, 2000 (87)
3	SC_JCM	ss3716843	Sep 28, 2001 (100)
4	WI_SSAHASNP	ss11566519	Jul 11, 2003 (116)
5	BCM_SSAHASNP	ss14188041	Dec 05, 2003 (119)
6	SSAHASNP	ss21968891	Apr 05, 2004 (121)
7	AFFY	ss65954628	Dec 01, 2006 (127)
8	ILLUMINA	ss75193069	Dec 07, 2007 (129)
9	HGSV	ss77385687	Dec 07, 2007 (129)
10	HGSV	ss78273469	Dec 07, 2007 (129)
11	HGSV	ss81394308	Dec 15, 2007 (130)
12	BCMHGSC_JDW	ss92320791	Mar 24, 2008 (129)
13	HUMANGENOME_JCVI	ss99140623	Feb 05, 2009 (130)
14	BGI	ss106305485	Feb 05, 2009 (130)
15	1000GENOMES	ss111110495	Jan 25, 2009 (130)
16	1000GENOMES	ss112564425	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss117319285	Feb 14, 2009 (130)
18	KRIBB_YJKIM	ss119368999	Dec 01, 2009 (131)
19	ENSEMBL	ss133866175	Dec 01, 2009 (131)
20	ENSEMBL	ss139218446	Dec 01, 2009 (131)
21	GMI	ss156329086	Dec 01, 2009 (131)
22	COMPLETE_GENOMICS	ss162709605	Jul 04, 2010 (132)
23	COMPLETE_GENOMICS	ss164572349	Jul 04, 2010 (132)
24	ILLUMINA	ss174729638	Jul 04, 2010 (132)
25	BUSHMAN	ss203336176	Jul 04, 2010 (132)
26	BCM-HGSC-SUB	ss206079431	Jul 04, 2010 (132)
27	1000GENOMES	ss220492122	Jul 14, 2010 (132)
28	1000GENOMES	ss232079327	Jul 14, 2010 (132)
29	1000GENOMES	ss239440291	Jul 15, 2010 (132)
30	GMI	ss277395629	May 04, 2012 (137)
31	GMI	ss284769977	Apr 25, 2013 (138)
32	PJP	ss292944619	May 09, 2011 (134)
33	ILLUMINA	ss410954968	Sep 17, 2011 (135)
34	ILLUMINA	ss537559137	Sep 08, 2015 (146)
35	TISHKOFF	ss557019079	Apr 25, 2013 (138)
36	SSMP	ss650750718	Apr 25, 2013 (138)
37	EVA-GONL	ss979287214	Aug 21, 2014 (142)
38	JMKIDD_LAB	ss1070926736	Aug 21, 2014 (142)
39	1000GENOMES	ss1306645307	Aug 21, 2014 (142)
40	DDI	ss1429624334	Apr 01, 2015 (144)
41	EVA_GENOME_DK	ss1580230847	Apr 01, 2015 (144)
42	EVA_DECODE	ss1588778270	Apr 01, 2015 (144)
43	EVA_UK10K_ALSPAC	ss1608470071	Apr 01, 2015 (144)
44	EVA_UK10K_TWINSUK	ss1651464104	Apr 01, 2015 (144)
45	EVA_SVP	ss1712621084	Apr 01, 2015 (144)
46	HAMMER_LAB	ss1800203066	Sep 08, 2015 (146)
47	WEILL_CORNELL_DGM	ss1922510857	Feb 12, 2016 (147)
48	JJLAB	ss2021826402	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2149922775	Dec 20, 2016 (150)
50	HUMAN_LONGEVITY	ss2256842698	Dec 20, 2016 (150)
51	GRF	ss2705336280	Nov 08, 2017 (151)
52	GNOMAD	ss2800521612	Nov 08, 2017 (151)
53	SWEGEN	ss2993390612	Nov 08, 2017 (151)
54	BIOINF_KMB_FNS_UNIBA	ss3024680906	Nov 08, 2017 (151)
55	CSHL	ss3345322195	Nov 08, 2017 (151)
56	ILLUMINA	ss3628802647	Oct 12, 2018 (152)
57	ILLUMINA	ss3638448436	Oct 12, 2018 (152)
58	ILLUMINA	ss3643402849	Oct 12, 2018 (152)
59	URBANLAB	ss3647553023	Oct 12, 2018 (152)
60	EGCUT_WGS	ss3661321631	Jul 13, 2019 (153)
61	EVA_DECODE	ss3710524625	Jul 13, 2019 (153)
62	ACPOP	ss3730455730	Jul 13, 2019 (153)
63	EVA	ss3760841521	Jul 13, 2019 (153)
64	PACBIO	ss3784496634	Jul 13, 2019 (153)
65	PACBIO	ss3789985300	Jul 13, 2019 (153)
66	PACBIO	ss3794859891	Jul 13, 2019 (153)
67	KHV_HUMAN_GENOMES	ss3803975582	Jul 13, 2019 (153)
68	EVA	ss3828134358	Apr 25, 2020 (154)
69	EVA	ss3837500318	Apr 25, 2020 (154)
70	EVA	ss3842931579	Apr 25, 2020 (154)
71	SGDP_PRJ	ss3857226324	Apr 25, 2020 (154)
72	KRGDB	ss3903264112	Apr 25, 2020 (154)
73	KOGIC	ss3952647759	Apr 25, 2020 (154)
74	EVA	ss3985028366	Apr 26, 2021 (155)
75	TOPMED	ss4587878033	Apr 26, 2021 (155)
76	TOMMO_GENOMICS	ss5162130986	Apr 26, 2021 (155)
77	1000G_HIGH_COVERAGE	ss5256450972	Oct 12, 2022 (156)
78	EVA	ss5344050074	Oct 12, 2022 (156)
79	HUGCELL_USP	ss5455547403	Oct 12, 2022 (156)
80	1000G_HIGH_COVERAGE	ss5536114137	Oct 12, 2022 (156)
81	SANFORD_IMAGENETICS	ss5633431414	Oct 12, 2022 (156)
82	TOMMO_GENOMICS	ss5695167520	Oct 12, 2022 (156)
83	YY_MCH	ss5804351374	Oct 12, 2022 (156)
84	EVA	ss5826642638	Oct 12, 2022 (156)
85	EVA	ss5853888184	Oct 12, 2022 (156)
86	EVA	ss5871490950	Oct 12, 2022 (156)
87	EVA	ss5961791618	Oct 12, 2022 (156)
88	1000Genomes	NC_000003.11 - 148399604	Oct 12, 2018 (152)
89	1000Genomes_30x	NC_000003.12 - 148681817	Oct 12, 2022 (156)
90	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 148399604	Oct 12, 2018 (152)
91	Genetic variation in the Estonian population	NC_000003.11 - 148399604	Oct 12, 2018 (152)
92	The Danish reference pan genome	NC_000003.11 - 148399604	Apr 25, 2020 (154)
93	gnomAD - Genomes	NC_000003.12 - 148681817	Apr 26, 2021 (155)
94	Genome of the Netherlands Release 5	NC_000003.11 - 148399604	Apr 25, 2020 (154)
95	HapMap	NC_000003.12 - 148681817	Apr 25, 2020 (154)
96	KOREAN population from KRGDB	NC_000003.11 - 148399604	Apr 25, 2020 (154)
97	Korean Genome Project	NC_000003.12 - 148681817	Apr 25, 2020 (154)
98	Northern Sweden	NC_000003.11 - 148399604	Jul 13, 2019 (153)
99	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000003.11 - 148399604	Apr 26, 2021 (155)
100	Qatari	NC_000003.11 - 148399604	Apr 25, 2020 (154)
101	SGDP_PRJ	NC_000003.11 - 148399604	Apr 25, 2020 (154)
102	Siberian	NC_000003.11 - 148399604	Apr 25, 2020 (154)
103	8.3KJPN	NC_000003.11 - 148399604	Apr 26, 2021 (155)
104	14KJPN	NC_000003.12 - 148681817	Oct 12, 2022 (156)
105	TopMed	NC_000003.12 - 148681817	Apr 26, 2021 (155)
106	UK 10K study - Twins	NC_000003.11 - 148399604	Oct 12, 2018 (152)
107	A Vietnamese Genetic Variation Database	NC_000003.11 - 148399604	Jul 13, 2019 (153)
108	ALFA	NC_000003.12 - 148681817	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)
rs58451614	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10441506, ss3903264112	NC_000003.11:148399603:T:A	NC_000003.12:148681816:T:A	(self)
8010719842	NC_000003.12:148681816:T:A	NC_000003.12:148681816:T:A	(self)
ss77385687, ss78273469, ss81394308	NC_000003.9:149882301:T:C	NC_000003.12:148681816:T:C	(self)
ss92320791, ss111110495, ss112564425, ss117319285, ss162709605, ss164572349, ss203336176, ss206079431, ss277395629, ss284769977, ss292944619, ss1588778270, ss1712621084, ss3643402849	NC_000003.10:149882293:T:C	NC_000003.12:148681816:T:C	(self)
17926067, 9983365, 7059879, 6395786, 4385790, 10441506, 3740595, 254293, 4552787, 9243304, 2439129, 20100293, 9983365, 2177558, ss220492122, ss232079327, ss239440291, ss537559137, ss557019079, ss650750718, ss979287214, ss1070926736, ss1306645307, ss1429624334, ss1580230847, ss1608470071, ss1651464104, ss1800203066, ss1922510857, ss2021826402, ss2149922775, ss2705336280, ss2800521612, ss2993390612, ss3345322195, ss3628802647, ss3638448436, ss3661321631, ss3730455730, ss3760841521, ss3784496634, ss3789985300, ss3794859891, ss3828134358, ss3837500318, ss3857226324, ss3903264112, ss3985028366, ss5162130986, ss5344050074, ss5633431414, ss5826642638, ss5961791618	NC_000003.11:148399603:T:C	NC_000003.12:148681816:T:C	(self)
23640072, 127355119, 2480530, 9025760, 29004624, 425255588, 8010719842, ss2256842698, ss3024680906, ss3647553023, ss3710524625, ss3803975582, ss3842931579, ss3952647759, ss4587878033, ss5256450972, ss5455547403, ss5536114137, ss5695167520, ss5804351374, ss5853888184, ss5871490950	NC_000003.12:148681816:T:C	NC_000003.12:148681816:T:C	(self)
ss11566519	NT_005612.13:54799139:T:C	NC_000003.12:148681816:T:C	(self)
ss14188041, ss21968891	NT_005612.14:54894757:T:C	NC_000003.12:148681816:T:C	(self)
ss1067858, ss1981575, ss3716843, ss65954628, ss75193069, ss99140623, ss106305485, ss119368999, ss133866175, ss139218446, ss156329086, ss174729638, ss410954968	NT_005612.16:54894749:T:C	NC_000003.12:148681816:T:C	(self)
10441506, ss3903264112	NC_000003.11:148399603:T:G	NC_000003.12:148681816:T:G	(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 rs813992

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

rs813992