Name: rs978379
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.

rs978379

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:52339384 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.430262 (113886/264690, TOPMED)
T=0.419318 (58728/140056, GnomAD)
A=0.30646 (8660/28258, 14KJPN) (+ 17 more)
T=0.40228 (7599/18890, ALFA)
A=0.30579 (5125/16760, 8.3KJPN)
T=0.4717 (3021/6404, 1000G_30x)
T=0.4714 (2361/5008, 1000G)
T=0.4234 (1897/4480, Estonian)
T=0.3633 (1400/3854, ALSPAC)
T=0.3687 (1367/3708, TWINSUK)
A=0.3648 (1069/2930, KOREAN)
A=0.3515 (644/1832, Korea1K)
T=0.4724 (838/1774, HapMap)
T=0.342 (341/998, GoNL)
T=0.322 (193/600, NorthernSweden)
A=0.325 (130/400, SGDP_PRJ)
T=0.296 (64/216, Qatari)
A=0.307 (65/212, Vietnamese)
T=0.30 (12/40, GENOME_DK)
A=0.33 (12/36, 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	A=0.59772	T=0.40228	0.361673	0.166226	0.472102	2
European	Sub	14286	A=0.62306	T=0.37694	0.388212	0.142097	0.469691	0
African	Sub	2946	A=0.5244	T=0.4756	0.275628	0.226748	0.497624	0
African Others	Sub	114	A=0.526	T=0.474	0.280702	0.22807	0.491228	0
African American	Sub	2832	A=0.5244	T=0.4756	0.275424	0.226695	0.497881	0
Asian	Sub	112	A=0.321	T=0.679	0.107143	0.464286	0.428571	0
East Asian	Sub	86	A=0.30	T=0.70	0.116279	0.511628	0.372093	0
Other Asian	Sub	26	A=0.38	T=0.62	0.076923	0.307692	0.615385	1
Latin American 1	Sub	146	A=0.671	T=0.329	0.465753	0.123288	0.410959	0
Latin American 2	Sub	610	A=0.428	T=0.572	0.193443	0.337705	0.468852	0
South Asian	Sub	98	A=0.66	T=0.34	0.510204	0.183673	0.306122	3
Other	Sub	692	A=0.556	T=0.444	0.32659	0.213873	0.459538	1

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=0.569738	T=0.430262
gnomAD - Genomes	Global	Study-wide	140056	A=0.580682	T=0.419318
gnomAD - Genomes	European	Sub	75866	A=0.63061	T=0.36939
gnomAD - Genomes	African	Sub	41956	A=0.52426	T=0.47574
gnomAD - Genomes	American	Sub	13634	A=0.50990	T=0.49010
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.6496	T=0.3504
gnomAD - Genomes	East Asian	Sub	3126	A=0.3698	T=0.6302
gnomAD - Genomes	Other	Sub	2152	A=0.5688	T=0.4312
14KJPN	JAPANESE	Study-wide	28258	A=0.30646	T=0.69354
Allele Frequency Aggregator	Total	Global	18890	A=0.59772	T=0.40228
Allele Frequency Aggregator	European	Sub	14286	A=0.62306	T=0.37694
Allele Frequency Aggregator	African	Sub	2946	A=0.5244	T=0.4756
Allele Frequency Aggregator	Other	Sub	692	A=0.556	T=0.444
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.428	T=0.572
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.671	T=0.329
Allele Frequency Aggregator	Asian	Sub	112	A=0.321	T=0.679
Allele Frequency Aggregator	South Asian	Sub	98	A=0.66	T=0.34
8.3KJPN	JAPANESE	Study-wide	16760	A=0.30579	T=0.69421
1000Genomes_30x	Global	Study-wide	6404	A=0.5283	T=0.4717
1000Genomes_30x	African	Sub	1786	A=0.5034	T=0.4966
1000Genomes_30x	Europe	Sub	1266	A=0.6414	T=0.3586
1000Genomes_30x	South Asian	Sub	1202	A=0.6839	T=0.3161
1000Genomes_30x	East Asian	Sub	1170	A=0.3162	T=0.6838
1000Genomes_30x	American	Sub	980	A=0.490	T=0.510
1000Genomes	Global	Study-wide	5008	A=0.5286	T=0.4714
1000Genomes	African	Sub	1322	A=0.5068	T=0.4932
1000Genomes	East Asian	Sub	1008	A=0.3185	T=0.6815
1000Genomes	Europe	Sub	1006	A=0.6392	T=0.3608
1000Genomes	South Asian	Sub	978	A=0.680	T=0.320
1000Genomes	American	Sub	694	A=0.501	T=0.499
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5766	T=0.4234
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.6367	T=0.3633
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.6313	T=0.3687
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.3648	T=0.6352
Korean Genome Project	KOREAN	Study-wide	1832	A=0.3515	T=0.6485
HapMap	Global	Study-wide	1774	A=0.5276	T=0.4724
HapMap	American	Sub	764	A=0.559	T=0.441
HapMap	African	Sub	582	A=0.545	T=0.455
HapMap	Asian	Sub	254	A=0.280	T=0.720
HapMap	Europe	Sub	174	A=0.695	T=0.305
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.658	T=0.342
Northern Sweden	ACPOP	Study-wide	600	A=0.678	T=0.322
SGDP_PRJ	Global	Study-wide	400	A=0.325	T=0.675
Qatari	Global	Study-wide	216	A=0.704	T=0.296
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.307	T=0.693
The Danish reference pan genome	Danish	Study-wide	40	A=0.70	T=0.30
Siberian	Global	Study-wide	36	A=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 12	NC_000012.12:g.52339384A>T
GRCh37.p13 chr 12	NC_000012.11:g.52733168A>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	A=	T
GRCh38.p14 chr 12	NC_000012.12:g.52339384=	NC_000012.12:g.52339384A>T
GRCh37.p13 chr 12	NC_000012.11:g.52733168=	NC_000012.11:g.52733168A>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#.

77 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1430852	Oct 05, 2000 (86)
2	TSC-CSHL	ss5563317	Oct 08, 2002 (108)
3	SC_JCM	ss6051696	Feb 20, 2003 (111)
4	SC_SNP	ss15938357	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss19235310	Feb 27, 2004 (120)
6	PERLEGEN	ss23300795	Sep 20, 2004 (123)
7	AFFY	ss66055757	Nov 30, 2006 (127)
8	AFFY	ss75967409	Dec 06, 2007 (129)
9	KRIBB_YJKIM	ss81448425	Dec 16, 2007 (130)
10	HGSV	ss83629822	Dec 14, 2007 (130)
11	HGSV	ss83930912	Dec 14, 2007 (130)
12	BCMHGSC_JDW	ss89153594	Mar 24, 2008 (129)
13	BGI	ss106806422	Feb 04, 2009 (130)
14	1000GENOMES	ss111943799	Jan 25, 2009 (130)
15	1000GENOMES	ss113546022	Jan 25, 2009 (130)
16	ILLUMINA-UK	ss118807482	Feb 14, 2009 (130)
17	ENSEMBL	ss133167979	Dec 01, 2009 (131)
18	ENSEMBL	ss161532294	Dec 01, 2009 (131)
19	AFFY	ss169793220	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss169847768	Jul 04, 2010 (132)
21	BUSHMAN	ss198183342	Jul 04, 2010 (132)
22	1000GENOMES	ss225755101	Jul 14, 2010 (132)
23	1000GENOMES	ss235936446	Jul 15, 2010 (132)
24	1000GENOMES	ss242495563	Jul 15, 2010 (132)
25	BL	ss255121240	May 09, 2011 (134)
26	GMI	ss281398075	May 04, 2012 (137)
27	GMI	ss286562099	Apr 25, 2013 (138)
28	PJP	ss291251273	May 09, 2011 (134)
29	TISHKOFF	ss563168535	Apr 25, 2013 (138)
30	SSMP	ss658724224	Apr 25, 2013 (138)
31	EVA-GONL	ss989537954	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1078463835	Aug 21, 2014 (142)
33	1000GENOMES	ss1345033537	Aug 21, 2014 (142)
34	DDI	ss1426934428	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1576285744	Apr 01, 2015 (144)
36	EVA_DECODE	ss1599209481	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1628600091	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1671594124	Apr 01, 2015 (144)
39	EVA_SVP	ss1713327906	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1807247416	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1932902399	Feb 12, 2016 (147)
42	GENOMED	ss1967590696	Jul 19, 2016 (147)
43	JJLAB	ss2027202225	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2155540281	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2189825298	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2628081857	Nov 08, 2017 (151)
47	GRF	ss2699883667	Nov 08, 2017 (151)
48	GNOMAD	ss2910554342	Nov 08, 2017 (151)
49	SWEGEN	ss3009695818	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3027409590	Nov 08, 2017 (151)
51	CSHL	ss3350066004	Nov 08, 2017 (151)
52	EGCUT_WGS	ss3676967969	Jul 13, 2019 (153)
53	EVA_DECODE	ss3693679738	Jul 13, 2019 (153)
54	ACPOP	ss3739025767	Jul 13, 2019 (153)
55	EVA	ss3750485425	Jul 13, 2019 (153)
56	PACBIO	ss3787227913	Jul 13, 2019 (153)
57	PACBIO	ss3792329357	Jul 13, 2019 (153)
58	PACBIO	ss3797212143	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3815814669	Jul 13, 2019 (153)
60	EVA	ss3833125180	Apr 27, 2020 (154)
61	SGDP_PRJ	ss3878283090	Apr 27, 2020 (154)
62	KRGDB	ss3926916114	Apr 27, 2020 (154)
63	KOGIC	ss3971943944	Apr 27, 2020 (154)
64	TOPMED	ss4918449884	Apr 26, 2021 (155)
65	TOMMO_GENOMICS	ss5206342794	Apr 26, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5290825466	Oct 13, 2022 (156)
67	EVA	ss5405664953	Oct 13, 2022 (156)
68	HUGCELL_USP	ss5485577093	Oct 13, 2022 (156)
69	EVA	ss5510705808	Oct 13, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5588319873	Oct 13, 2022 (156)
71	SANFORD_IMAGENETICS	ss5653162327	Oct 13, 2022 (156)
72	TOMMO_GENOMICS	ss5756140804	Oct 13, 2022 (156)
73	YY_MCH	ss5813302370	Oct 13, 2022 (156)
74	EVA	ss5837972329	Oct 13, 2022 (156)
75	EVA	ss5850383128	Oct 13, 2022 (156)
76	EVA	ss5904411290	Oct 13, 2022 (156)
77	EVA	ss5944525563	Oct 13, 2022 (156)
78	1000Genomes	NC_000012.11 - 52733168	Oct 12, 2018 (152)
79	1000Genomes_30x	NC_000012.12 - 52339384	Oct 13, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 52733168	Oct 12, 2018 (152)
81	Genetic variation in the Estonian population	NC_000012.11 - 52733168	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000012.11 - 52733168	Apr 27, 2020 (154)
83	gnomAD - Genomes	NC_000012.12 - 52339384	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000012.11 - 52733168	Apr 27, 2020 (154)
85	HapMap	NC_000012.12 - 52339384	Apr 27, 2020 (154)
86	KOREAN population from KRGDB	NC_000012.11 - 52733168	Apr 27, 2020 (154)
87	Korean Genome Project	NC_000012.12 - 52339384	Apr 27, 2020 (154)
88	Northern Sweden	NC_000012.11 - 52733168	Jul 13, 2019 (153)
89	Qatari	NC_000012.11 - 52733168	Apr 27, 2020 (154)
90	SGDP_PRJ	NC_000012.11 - 52733168	Apr 27, 2020 (154)
91	Siberian	NC_000012.11 - 52733168	Apr 27, 2020 (154)
92	8.3KJPN	NC_000012.11 - 52733168	Apr 26, 2021 (155)
93	14KJPN	NC_000012.12 - 52339384	Oct 13, 2022 (156)
94	TopMed	NC_000012.12 - 52339384	Apr 26, 2021 (155)
95	UK 10K study - Twins	NC_000012.11 - 52733168	Oct 12, 2018 (152)
96	A Vietnamese Genetic Variation Database	NC_000012.11 - 52733168	Jul 13, 2019 (153)
97	ALFA	NC_000012.12 - 52339384	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)
rs57648877	May 23, 2008 (130)
rs61538619	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss83629822, ss83930912	NC_000012.9:51019434:A:T	NC_000012.12:52339383:A:T	(self)
ss66055757, ss75967409, ss89153594, ss111943799, ss113546022, ss118807482, ss169793220, ss169847768, ss198183342, ss255121240, ss281398075, ss286562099, ss291251273, ss1599209481, ss1713327906	NC_000012.10:51019434:A:T	NC_000012.12:52339383:A:T	(self)
57783252, 32085385, 22706217, 2965345, 14317786, 34093508, 12310632, 14944329, 30300070, 8056635, 64312101, 32085385, 7122739, ss225755101, ss235936446, ss242495563, ss563168535, ss658724224, ss989537954, ss1078463835, ss1345033537, ss1426934428, ss1576285744, ss1628600091, ss1671594124, ss1807247416, ss1932902399, ss1967590696, ss2027202225, ss2155540281, ss2628081857, ss2699883667, ss2910554342, ss3009695818, ss3350066004, ss3676967969, ss3739025767, ss3750485425, ss3787227913, ss3792329357, ss3797212143, ss3833125180, ss3878283090, ss3926916114, ss5206342794, ss5405664953, ss5510705808, ss5653162327, ss5837972329, ss5944525563	NC_000012.11:52733167:A:T	NC_000012.12:52339383:A:T	(self)
75845808, 407472201, 816901, 28321945, 89977908, 133995541, 7799303279, ss2189825298, ss3027409590, ss3693679738, ss3815814669, ss3971943944, ss4918449884, ss5290825466, ss5485577093, ss5588319873, ss5756140804, ss5813302370, ss5850383128, ss5904411290	NC_000012.12:52339383:A:T	NC_000012.12:52339383:A:T	(self)
ss15938357, ss19235310	NT_029419.10:14876473:A:T	NC_000012.12:52339383:A:T	(self)
ss1430852, ss5563317, ss6051696, ss23300795, ss81448425, ss106806422, ss133167979, ss161532294	NT_029419.12:14876473:A:T	NC_000012.12:52339383:A: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 rs978379

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

rs978379