Name: rs2977670
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.

rs2977670

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:788511 (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: G>A / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.26453 (7474/28254, 14KJPN)
G=0.26301 (4408/16760, 8.3KJPN)
G=0.2258 (1446/6404, 1000G_30x) (+ 12 more)
G=0.1669 (903/5412, ALFA)
G=0.2200 (1102/5008, 1000G)
G=0.0400 (154/3854, ALSPAC)
G=0.0440 (163/3708, TWINSUK)
G=0.2020 (592/2930, KOREAN)
G=0.034 (34/998, GoNL)
G=0.037 (22/600, NorthernSweden)
G=0.154 (75/488, SGDP_PRJ)
G=0.299 (94/314, HapMap)
G=0.190 (41/216, Qatari)
G=0.03 (1/40, GENOME_DK)
G=0.03 (1/30, 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	5412	G=0.1669	A=0.0000, C=0.8331, T=0.0000
European	Sub	4596	G=0.0668	A=0.0000, C=0.9332, T=0.0000
African	Sub	594	G=0.938	A=0.000, C=0.062, T=0.000
African Others	Sub	30	G=1.00	A=0.00, C=0.00, T=0.00
African American	Sub	564	G=0.934	A=0.000, C=0.066, T=0.000
Asian	Sub	2	G=1.0	A=0.0, C=0.0, T=0.0
East Asian	Sub	2	G=1.0	A=0.0, C=0.0, T=0.0
Other Asian	Sub	0	G=0	A=0, C=0, T=0
Latin American 1	Sub	8	G=1.0	A=0.0, C=0.0, T=0.0
Latin American 2	Sub	2	G=1.0	A=0.0, C=0.0, T=0.0
South Asian	Sub	0	G=0	A=0, C=0, T=0
Other	Sub	210	G=0.129	A=0.000, C=0.871, 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	28254	G=0.26453	C=0.73547
8.3KJPN	JAPANESE	Study-wide	16760	G=0.26301	C=0.73699
1000Genomes_30x	Global	Study-wide	6404	G=0.2258	C=0.7742
1000Genomes_30x	African	Sub	1786	G=0.5168	C=0.4832
1000Genomes_30x	Europe	Sub	1266	G=0.0537	C=0.9463
1000Genomes_30x	South Asian	Sub	1202	G=0.0674	C=0.9326
1000Genomes_30x	East Asian	Sub	1170	G=0.2085	C=0.7915
1000Genomes_30x	American	Sub	980	G=0.133	C=0.867
Allele Frequency Aggregator	Total	Global	5412	G=0.1669	A=0.0000, C=0.8331, T=0.0000
Allele Frequency Aggregator	European	Sub	4596	G=0.0668	A=0.0000, C=0.9332, T=0.0000
Allele Frequency Aggregator	African	Sub	594	G=0.938	A=0.000, C=0.062, T=0.000
Allele Frequency Aggregator	Other	Sub	210	G=0.129	A=0.000, C=0.871, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	8	G=1.0	A=0.0, C=0.0, T=0.0
Allele Frequency Aggregator	Latin American 2	Sub	2	G=1.0	A=0.0, C=0.0, T=0.0
Allele Frequency Aggregator	Asian	Sub	2	G=1.0	A=0.0, C=0.0, T=0.0
Allele Frequency Aggregator	South Asian	Sub	0	G=0	A=0, C=0, T=0
1000Genomes	Global	Study-wide	5008	G=0.2200	C=0.7800
1000Genomes	African	Sub	1322	G=0.5151	C=0.4849
1000Genomes	East Asian	Sub	1008	G=0.2083	C=0.7917
1000Genomes	Europe	Sub	1006	G=0.0517	C=0.9483
1000Genomes	South Asian	Sub	978	G=0.070	C=0.930
1000Genomes	American	Sub	694	G=0.131	C=0.869
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.0400	C=0.9600
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.0440	C=0.9560
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2020	A=0.0000, C=0.7980
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.034	C=0.966
Northern Sweden	ACPOP	Study-wide	600	G=0.037	C=0.963
SGDP_PRJ	Global	Study-wide	488	G=0.154	C=0.846
HapMap	Global	Study-wide	314	G=0.299	C=0.701
HapMap	African	Sub	118	G=0.492	C=0.508
HapMap	American	Sub	112	G=0.071	C=0.929
HapMap	Asian	Sub	84	G=0.33	C=0.67
Qatari	Global	Study-wide	216	G=0.190	C=0.810
The Danish reference pan genome	Danish	Study-wide	40	G=0.03	C=0.97
Siberian	Global	Study-wide	30	G=0.03	C=0.97

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.788511G>A
GRCh38.p14 chr 1	NC_000001.11:g.788511G>C
GRCh38.p14 chr 1	NC_000001.11:g.788511G>T
GRCh37.p13 chr 1	NC_000001.10:g.723891G>A
GRCh37.p13 chr 1	NC_000001.10:g.723891G>C
GRCh37.p13 chr 1	NC_000001.10:g.723891G>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	G=	A	C	T
GRCh38.p14 chr 1	NC_000001.11:g.788511=	NC_000001.11:g.788511G>A	NC_000001.11:g.788511G>C	NC_000001.11:g.788511G>T
GRCh37.p13 chr 1	NC_000001.10:g.723891=	NC_000001.10:g.723891G>A	NC_000001.10:g.723891G>C	NC_000001.10:g.723891G>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#.

64 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4191663	Nov 05, 2001 (101)
2	WI_SSAHASNP	ss6851725	Feb 20, 2003 (111)
3	CSHL-HAPMAP	ss16399802	Feb 27, 2004 (120)
4	ILLUMINA	ss65798767	Oct 15, 2006 (127)
5	HGSV	ss78163595	Dec 06, 2007 (129)
6	HGSV	ss78764316	Dec 06, 2007 (129)
7	BCMHGSC_JDW	ss87155374	Mar 23, 2008 (129)
8	HUMANGENOME_JCVI	ss97913175	Feb 05, 2009 (130)
9	BGI	ss105111637	Dec 01, 2009 (131)
10	ILLUMINA-UK	ss118438178	Feb 14, 2009 (130)
11	ENSEMBL	ss137751620	Dec 01, 2009 (131)
12	ENSEMBL	ss138905911	Dec 01, 2009 (131)
13	GMI	ss154522241	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss163702668	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss205287261	Jul 04, 2010 (132)
16	1000GENOMES	ss218190347	Jul 14, 2010 (132)
17	1000GENOMES	ss230395410	Jul 14, 2010 (132)
18	1000GENOMES	ss238114944	Jul 15, 2010 (132)
19	BL	ss252864003	May 09, 2011 (134)
20	GMI	ss275680560	May 04, 2012 (137)
21	GMI	ss283987305	Apr 25, 2013 (138)
22	PJP	ss290493755	May 09, 2011 (134)
23	SSMP	ss647515880	Apr 25, 2013 (138)
24	EVA-GONL	ss974769091	Aug 21, 2014 (142)
25	1000GENOMES	ss1289338094	Aug 21, 2014 (142)
26	DDI	ss1425684731	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1573851066	Apr 01, 2015 (144)
28	EVA_DECODE	ss1584129360	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1599378241	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1642372274	Apr 01, 2015 (144)
31	WEILL_CORNELL_DGM	ss1917959781	Feb 12, 2016 (147)
32	GENOMED	ss1966667310	Jul 19, 2016 (147)
33	JJLAB	ss2019498276	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2147483833	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2624264731	Nov 08, 2017 (151)
36	GRF	ss2697374049	Nov 08, 2017 (151)
37	GNOMAD	ss2750633525	Nov 08, 2017 (151)
38	SWEGEN	ss2986147808	Nov 08, 2017 (151)
39	CSHL	ss3343272203	Nov 08, 2017 (151)
40	URBANLAB	ss3646581105	Oct 11, 2018 (152)
41	EVA_DECODE	ss3685991680	Jul 12, 2019 (153)
42	ACPOP	ss3726716018	Jul 12, 2019 (153)
43	EVA	ss3745720728	Jul 12, 2019 (153)
44	PACBIO	ss3783302035	Jul 12, 2019 (153)
45	PACBIO	ss3788979914	Jul 12, 2019 (153)
46	PACBIO	ss3793852451	Jul 12, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3798743140	Jul 12, 2019 (153)
48	EVA	ss3825981376	Apr 25, 2020 (154)
49	EVA	ss3836378320	Apr 25, 2020 (154)
50	EVA	ss3841782318	Apr 25, 2020 (154)
51	SGDP_PRJ	ss3847993911	Apr 25, 2020 (154)
52	KRGDB	ss3892833348	Apr 25, 2020 (154)
53	TOMMO_GENOMICS	ss5142049614	Apr 25, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5240861537	Oct 12, 2022 (156)
55	EVA	ss5316180906	Oct 12, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5512485870	Oct 12, 2022 (156)
57	SANFORD_IMAGENETICS	ss5624747957	Oct 12, 2022 (156)
58	TOMMO_GENOMICS	ss5666187959	Oct 12, 2022 (156)
59	YY_MCH	ss5800243167	Oct 12, 2022 (156)
60	EVA	ss5831417677	Oct 12, 2022 (156)
61	EVA	ss5848748808	Oct 12, 2022 (156)
62	EVA	ss5906704159	Oct 12, 2022 (156)
63	EVA	ss5936582170	Oct 12, 2022 (156)
64	EVA	ss5979259131	Oct 12, 2022 (156)
65	1000Genomes	NC_000001.10 - 723891	Oct 11, 2018 (152)
66	1000Genomes_30x	NC_000001.11 - 788511	Oct 12, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 723891	Oct 11, 2018 (152)
68	The Danish reference pan genome	NC_000001.10 - 723891	Apr 25, 2020 (154)
69	gnomAD - Genomes Submission ignored due to conflicting rows: Row 54890 (NC_000001.11:788510:G:C 114790/139970) Row 54891 (NC_000001.11:788510:G:T 2/140080)	-	Apr 25, 2021 (155)
70	gnomAD - Genomes Submission ignored due to conflicting rows: Row 54890 (NC_000001.11:788510:G:C 114790/139970) Row 54891 (NC_000001.11:788510:G:T 2/140080)	-	Apr 25, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000001.10 - 723891	Apr 25, 2020 (154)
72	HapMap	NC_000001.11 - 788511	Apr 25, 2020 (154)
73	KOREAN population from KRGDB	NC_000001.10 - 723891	Apr 25, 2020 (154)
74	Northern Sweden	NC_000001.10 - 723891	Jul 12, 2019 (153)
75	Qatari	NC_000001.10 - 723891	Apr 25, 2020 (154)
76	SGDP_PRJ	NC_000001.10 - 723891	Apr 25, 2020 (154)
77	Siberian	NC_000001.10 - 723891	Apr 25, 2020 (154)
78	8.3KJPN	NC_000001.10 - 723891	Apr 25, 2021 (155)
79	14KJPN	NC_000001.11 - 788511	Oct 12, 2022 (156)
80	UK 10K study - Twins	NC_000001.10 - 723891	Oct 11, 2018 (152)
81	ALFA	NC_000001.11 - 788511	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
10742, ss3892833348	NC_000001.10:723890:G:A	NC_000001.11:788510:G:A	(self)
14464662077	NC_000001.11:788510:G:A	NC_000001.11:788510:G:A	(self)
ss78163595, ss78764316	NC_000001.8:763753:G:C	NC_000001.11:788510:G:C	(self)
ss87155374, ss118438178, ss163702668, ss205287261, ss252864003, ss275680560, ss283987305, ss290493755, ss1584129360	NC_000001.9:713753:G:C	NC_000001.11:788510:G:C	(self)
2770, 97, 1358300, 203, 10742, 883, 1711, 10891, 187, 18921, 97, ss218190347, ss230395410, ss238114944, ss647515880, ss974769091, ss1289338094, ss1425684731, ss1573851066, ss1599378241, ss1642372274, ss1917959781, ss1966667310, ss2019498276, ss2147483833, ss2624264731, ss2697374049, ss2750633525, ss2986147808, ss3343272203, ss3726716018, ss3745720728, ss3783302035, ss3788979914, ss3793852451, ss3825981376, ss3836378320, ss3847993911, ss3892833348, ss5142049614, ss5316180906, ss5624747957, ss5831417677, ss5936582170, ss5979259131	NC_000001.10:723890:G:C	NC_000001.11:788510:G:C	(self)
11805, 30, 25063, 14464662077, ss3646581105, ss3685991680, ss3798743140, ss3841782318, ss5240861537, ss5512485870, ss5666187959, ss5800243167, ss5848748808, ss5906704159	NC_000001.11:788510:G:C	NC_000001.11:788510:G:C	(self)
ss4191663, ss6851725, ss65798767, ss97913175, ss105111637, ss137751620, ss138905911, ss154522241	NT_004350.19:202522:G:C	NC_000001.11:788510:G:C	(self)
ss16399802	NT_034471.3:202522:G:C	NC_000001.11:788510:G:C	(self)
14464662077	NC_000001.11:788510:G:T	NC_000001.11:788510:G: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 rs2977670

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

rs2977670