Name: rs813978
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.

rs813978

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:192929068 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.454407 (120277/264690, TOPMED)
G=0.443210 (62021/139936, GnomAD)
G=0.44635 (12613/28258, 14KJPN) (+ 17 more)
G=0.43367 (8192/18890, ALFA)
G=0.44487 (7456/16760, 8.3KJPN)
G=0.4557 (2918/6404, 1000G_30x)
G=0.4575 (2291/5008, 1000G)
G=0.3737 (1674/4480, Estonian)
G=0.4447 (1714/3854, ALSPAC)
G=0.4515 (1674/3708, TWINSUK)
G=0.3778 (1107/2930, KOREAN)
G=0.3706 (679/1832, Korea1K)
G=0.4382 (730/1666, HapMap)
G=0.454 (453/998, GoNL)
G=0.467 (280/600, NorthernSweden)
C=0.339 (141/416, SGDP_PRJ)
C=0.380 (82/216, Qatari)
G=0.352 (76/216, Vietnamese)
C=0.33 (14/42, Siberian)
C=0.47 (19/40, GENOME_DK)

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	18890	C=0.56633	G=0.43367
European	Sub	14286	C=0.57014	G=0.42986
African	Sub	2946	C=0.5784	G=0.4216
African Others	Sub	114	C=0.588	G=0.412
African American	Sub	2832	C=0.5780	G=0.4220
Asian	Sub	112	C=0.688	G=0.312
East Asian	Sub	86	C=0.67	G=0.33
Other Asian	Sub	26	C=0.73	G=0.27
Latin American 1	Sub	146	C=0.452	G=0.548
Latin American 2	Sub	610	C=0.405	G=0.595
South Asian	Sub	98	C=0.49	G=0.51
Other	Sub	692	C=0.594	G=0.406

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=0.545593	G=0.454407
gnomAD - Genomes	Global	Study-wide	139936	C=0.556790	G=0.443210
gnomAD - Genomes	European	Sub	75800	C=0.55365	G=0.44635
gnomAD - Genomes	African	Sub	41918	C=0.58307	G=0.41693
gnomAD - Genomes	American	Sub	13624	C=0.48246	G=0.51754
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.5196	G=0.4804
gnomAD - Genomes	East Asian	Sub	3118	C=0.6600	G=0.3400
gnomAD - Genomes	Other	Sub	2154	C=0.5339	G=0.4661
14KJPN	JAPANESE	Study-wide	28258	C=0.55365	G=0.44635
Allele Frequency Aggregator	Total	Global	18890	C=0.56633	G=0.43367
Allele Frequency Aggregator	European	Sub	14286	C=0.57014	G=0.42986
Allele Frequency Aggregator	African	Sub	2946	C=0.5784	G=0.4216
Allele Frequency Aggregator	Other	Sub	692	C=0.594	G=0.406
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.405	G=0.595
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.452	G=0.548
Allele Frequency Aggregator	Asian	Sub	112	C=0.688	G=0.312
Allele Frequency Aggregator	South Asian	Sub	98	C=0.49	G=0.51
8.3KJPN	JAPANESE	Study-wide	16760	C=0.55513	G=0.44487
1000Genomes_30x	Global	Study-wide	6404	C=0.5443	G=0.4557
1000Genomes_30x	African	Sub	1786	C=0.6025	G=0.3975
1000Genomes_30x	Europe	Sub	1266	C=0.5269	G=0.4731
1000Genomes_30x	South Asian	Sub	1202	C=0.4867	G=0.5133
1000Genomes_30x	East Asian	Sub	1170	C=0.6350	G=0.3650
1000Genomes_30x	American	Sub	980	C=0.423	G=0.577
1000Genomes	Global	Study-wide	5008	C=0.5425	G=0.4575
1000Genomes	African	Sub	1322	C=0.5855	G=0.4145
1000Genomes	East Asian	Sub	1008	C=0.6399	G=0.3601
1000Genomes	Europe	Sub	1006	C=0.5239	G=0.4761
1000Genomes	South Asian	Sub	978	C=0.484	G=0.516
1000Genomes	American	Sub	694	C=0.429	G=0.571
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6263	G=0.3737
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5553	G=0.4447
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5485	G=0.4515
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6222	G=0.3778
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6294	G=0.3706
HapMap	Global	Study-wide	1666	C=0.5618	G=0.4382
HapMap	African	Sub	692	C=0.574	G=0.426
HapMap	American	Sub	544	C=0.540	G=0.460
HapMap	Asian	Sub	254	C=0.587	G=0.413
HapMap	Europe	Sub	176	C=0.545	G=0.455
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.546	G=0.454
Northern Sweden	ACPOP	Study-wide	600	C=0.533	G=0.467
SGDP_PRJ	Global	Study-wide	416	C=0.339	G=0.661
Qatari	Global	Study-wide	216	C=0.380	G=0.620
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.648	G=0.352
Siberian	Global	Study-wide	42	C=0.33	G=0.67
The Danish reference pan genome	Danish	Study-wide	40	C=0.47	G=0.53

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.192929068C>G
GRCh37.p13 chr 3	NC_000003.11:g.192646857C>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	C=	G
GRCh38.p14 chr 3	NC_000003.12:g.192929068=	NC_000003.12:g.192929068C>G
GRCh37.p13 chr 3	NC_000003.11:g.192646857=	NC_000003.11:g.192646857C>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#.

76 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1067831	Oct 05, 2000 (86)
2	TSC-CSHL	ss2187047	Oct 23, 2000 (89)
3	SC_JCM	ss3737506	Sep 28, 2001 (100)
4	WI_SSAHASNP	ss6455812	Feb 20, 2003 (111)
5	BCM_SSAHASNP	ss14213122	Dec 05, 2003 (119)
6	CSHL-HAPMAP	ss17753699	Feb 27, 2004 (120)
7	ABI	ss44391712	Mar 13, 2006 (126)
8	AFFY	ss66408414	Dec 01, 2006 (127)
9	AFFY	ss76163883	Dec 06, 2007 (129)
10	HGSV	ss78059541	Dec 06, 2007 (129)
11	KRIBB_YJKIM	ss81439187	Dec 15, 2007 (130)
12	HUMANGENOME_JCVI	ss96087797	Feb 04, 2009 (130)
13	BGI	ss104027131	Dec 01, 2009 (131)
14	1000GENOMES	ss111581011	Jan 25, 2009 (130)
15	1000GENOMES	ss112808727	Jan 25, 2009 (130)
16	ENSEMBL	ss161429009	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss165349273	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss167531907	Jul 04, 2010 (132)
19	AFFY	ss172683854	Jul 04, 2010 (132)
20	1000GENOMES	ss220664464	Jul 14, 2010 (132)
21	1000GENOMES	ss232203620	Jul 14, 2010 (132)
22	1000GENOMES	ss239536994	Jul 15, 2010 (132)
23	GMI	ss277514160	May 04, 2012 (137)
24	PJP	ss293003338	May 09, 2011 (134)
25	TISHKOFF	ss557217722	Apr 25, 2013 (138)
26	SSMP	ss650964321	Apr 25, 2013 (138)
27	EVA-GONL	ss979614001	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1071175562	Aug 21, 2014 (142)
29	1000GENOMES	ss1307869291	Aug 21, 2014 (142)
30	DDI	ss1429719710	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1580358246	Apr 01, 2015 (144)
32	EVA_DECODE	ss1589113173	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1609127139	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1652121172	Apr 01, 2015 (144)
35	EVA_SVP	ss1712642501	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1800692001	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1922836810	Feb 12, 2016 (147)
38	GENOMED	ss1969626103	Jul 19, 2016 (147)
39	JJLAB	ss2021994634	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2150095434	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2259409361	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2625497849	Nov 08, 2017 (151)
43	GRF	ss2705522740	Nov 08, 2017 (151)
44	GNOMAD	ss2804028917	Nov 08, 2017 (151)
45	SWEGEN	ss2993884376	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3024767266	Nov 08, 2017 (151)
47	CSHL	ss3345465592	Nov 08, 2017 (151)
48	URBANLAB	ss3647619532	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3661845444	Jul 13, 2019 (153)
50	EVA_DECODE	ss3711124207	Jul 13, 2019 (153)
51	ACPOP	ss3730725904	Jul 13, 2019 (153)
52	EVA	ss3761216262	Jul 13, 2019 (153)
53	PACBIO	ss3784578627	Jul 13, 2019 (153)
54	PACBIO	ss3790053886	Jul 13, 2019 (153)
55	PACBIO	ss3794928727	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3804356454	Jul 13, 2019 (153)
57	EVA	ss3828296894	Apr 25, 2020 (154)
58	EVA	ss3837580279	Apr 25, 2020 (154)
59	EVA	ss3843013234	Apr 25, 2020 (154)
60	SGDP_PRJ	ss3857881059	Apr 25, 2020 (154)
61	KRGDB	ss3903977212	Apr 25, 2020 (154)
62	KOGIC	ss3953234373	Apr 25, 2020 (154)
63	TOPMED	ss4598485906	Apr 26, 2021 (155)
64	TOMMO_GENOMICS	ss5163522660	Apr 26, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5257530078	Oct 13, 2022 (156)
66	EVA	ss5346011367	Oct 13, 2022 (156)
67	HUGCELL_USP	ss5456526329	Oct 13, 2022 (156)
68	EVA	ss5507356164	Oct 13, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5537748970	Oct 13, 2022 (156)
70	SANFORD_IMAGENETICS	ss5634052199	Oct 13, 2022 (156)
71	TOMMO_GENOMICS	ss5696957704	Oct 13, 2022 (156)
72	YY_MCH	ss5804618497	Oct 13, 2022 (156)
73	EVA	ss5827062284	Oct 13, 2022 (156)
74	EVA	ss5854023269	Oct 13, 2022 (156)
75	EVA	ss5872723803	Oct 13, 2022 (156)
76	EVA	ss5962438307	Oct 13, 2022 (156)
77	1000Genomes	NC_000003.11 - 192646857	Oct 12, 2018 (152)
78	1000Genomes_30x	NC_000003.12 - 192929068	Oct 13, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 192646857	Oct 12, 2018 (152)
80	Genetic variation in the Estonian population	NC_000003.11 - 192646857	Oct 12, 2018 (152)
81	The Danish reference pan genome	NC_000003.11 - 192646857	Apr 25, 2020 (154)
82	gnomAD - Genomes	NC_000003.12 - 192929068	Apr 26, 2021 (155)
83	Genome of the Netherlands Release 5	NC_000003.11 - 192646857	Apr 25, 2020 (154)
84	HapMap	NC_000003.12 - 192929068	Apr 25, 2020 (154)
85	KOREAN population from KRGDB	NC_000003.11 - 192646857	Apr 25, 2020 (154)
86	Korean Genome Project	NC_000003.12 - 192929068	Apr 25, 2020 (154)
87	Northern Sweden	NC_000003.11 - 192646857	Jul 13, 2019 (153)
88	Qatari	NC_000003.11 - 192646857	Apr 25, 2020 (154)
89	SGDP_PRJ	NC_000003.11 - 192646857	Apr 25, 2020 (154)
90	Siberian	NC_000003.11 - 192646857	Apr 25, 2020 (154)
91	8.3KJPN	NC_000003.11 - 192646857	Apr 26, 2021 (155)
92	14KJPN	NC_000003.12 - 192929068	Oct 13, 2022 (156)
93	TopMed	NC_000003.12 - 192929068	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000003.11 - 192646857	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000003.11 - 192646857	Jul 13, 2019 (153)
96	ALFA	NC_000003.12 - 192929068	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)
rs1392665	Nov 09, 2000 (89)
rs59372479	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78059541	NC_000003.9:194129558:C:G	NC_000003.12:192929067:C:G	(self)
ss66408414, ss76163883, ss111581011, ss112808727, ss165349273, ss167531907, ss172683854, ss277514160, ss293003338, ss1589113173, ss1712642501	NC_000003.10:194129550:C:G	NC_000003.12:192929067:C:G	(self)
19199087, 10707620, 7583692, 6523185, 4704305, 11154606, 4010769, 4878740, 9898039, 2611788, 21491967, 10707620, 2342090, ss220664464, ss232203620, ss239536994, ss557217722, ss650964321, ss979614001, ss1071175562, ss1307869291, ss1429719710, ss1580358246, ss1609127139, ss1652121172, ss1800692001, ss1922836810, ss1969626103, ss2021994634, ss2150095434, ss2625497849, ss2705522740, ss2804028917, ss2993884376, ss3345465592, ss3661845444, ss3730725904, ss3761216262, ss3784578627, ss3790053886, ss3794928727, ss3828296894, ss3837580279, ss3857881059, ss3903977212, ss5163522660, ss5346011367, ss5507356164, ss5634052199, ss5827062284, ss5962438307	NC_000003.11:192646856:C:G	NC_000003.12:192929067:C:G	(self)
25274905, 136317908, 2537329, 9612374, 30794808, 435863461, 139203501, ss2259409361, ss3024767266, ss3647619532, ss3711124207, ss3804356454, ss3843013234, ss3953234373, ss4598485906, ss5257530078, ss5456526329, ss5537748970, ss5696957704, ss5804618497, ss5854023269, ss5872723803	NC_000003.12:192929067:C:G	NC_000003.12:192929067:C:G	(self)
ss14213122, ss17753699	NT_005612.14:99142014:C:G	NC_000003.12:192929067:C:G	(self)
ss1067831, ss2187047, ss3737506, ss6455812, ss44391712, ss81439187, ss96087797, ss104027131, ss161429009	NT_005612.16:99142002:C:G	NC_000003.12:192929067:C: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 rs813978

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

rs813978