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dbSNP Short Genetic Variations

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.

rs4970387

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:881854 (GRCh38.p13) 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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.063878 (16908/264690, TOPMED)
A=0.054119 (7587/140192, GnomAD)
A=0.02856 (506/17716, ALFA) (+ 12 more)
A=0.16736 (2805/16760, 8.3KJPN)
A=0.0909 (455/5008, 1000G)
A=0.0031 (12/3854, ALSPAC)
A=0.0038 (14/3708, TWINSUK)
A=0.1618 (474/2930, KOREAN)
A=0.003 (3/998, GoNL)
A=0.000 (0/600, NorthernSweden)
A=0.101 (53/526, SGDP_PRJ)
A=0.088 (19/216, Qatari)
A=0.192 (41/214, Vietnamese)
A=0.07 (4/56, Siberian)
A=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
Help

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.p13 chr 1 NC_000001.11:g.881854A>C
GRCh38.p13 chr 1 NC_000001.11:g.881854A>G
GRCh38.p13 chr 1 NC_000001.11:g.881854A>T
GRCh37.p13 chr 1 NC_000001.10:g.817234A>C
GRCh37.p13 chr 1 NC_000001.10:g.817234A>G
GRCh37.p13 chr 1 NC_000001.10:g.817234A>T
Help

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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 17716 A=0.02856 G=0.00000, T=0.97144
European Sub 13630 A=0.00396 G=0.00000, T=0.99604
African Sub 2432 A=0.1349 G=0.0000, T=0.8651
African Others Sub 90 A=0.16 G=0.00, T=0.84
African American Sub 2342 A=0.1341 G=0.0000, T=0.8659
Asian Sub 112 A=0.143 G=0.000, T=0.857
East Asian Sub 86 A=0.16 G=0.00, T=0.84
Other Asian Sub 26 A=0.08 G=0.00, T=0.92
Latin American 1 Sub 146 A=0.089 G=0.000, T=0.911
Latin American 2 Sub 610 A=0.080 G=0.000, T=0.920
South Asian Sub 98 A=0.04 G=0.00, T=0.96
Other Sub 688 A=0.061 G=0.000, T=0.939


Help

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 A=0.063878 T=0.936122
gnomAD - Genomes Global Study-wide 140192 A=0.054119 T=0.945881
gnomAD - Genomes European Sub 75944 A=0.00263 T=0.99737
gnomAD - Genomes African Sub 41994 A=0.13659 T=0.86341
gnomAD - Genomes American Sub 13650 A=0.07304 T=0.92696
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.0090 T=0.9910
gnomAD - Genomes East Asian Sub 3130 A=0.1543 T=0.8457
gnomAD - Genomes Other Sub 2150 A=0.0656 T=0.9344
8.3KJPN JAPANESE Study-wide 16760 A=0.16736 T=0.83264
1000Genomes Global Study-wide 5008 A=0.0909 T=0.9091
1000Genomes African Sub 1322 A=0.1657 T=0.8343
1000Genomes East Asian Sub 1008 A=0.1478 T=0.8522
1000Genomes Europe Sub 1006 A=0.0040 T=0.9960
1000Genomes South Asian Sub 978 A=0.024 T=0.976
1000Genomes American Sub 694 A=0.086 T=0.914
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.0031 T=0.9969
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.0038 T=0.9962
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.1618 C=0.0000, T=0.8382
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.003 T=0.997
Northern Sweden ACPOP Study-wide 600 A=0.000 T=1.000
SGDP_PRJ Global Study-wide 526 A=0.101 T=0.899
Qatari Global Study-wide 216 A=0.088 T=0.912
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.192 T=0.808
Siberian Global Study-wide 56 A=0.07 T=0.93
The Danish reference pan genome Danish Study-wide 40 A=0.00 T=1.00
Help

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= C G T
GRCh38.p13 chr 1 NC_000001.11:g.881854= NC_000001.11:g.881854A>C NC_000001.11:g.881854A>G NC_000001.11:g.881854A>T
GRCh37.p13 chr 1 NC_000001.10:g.817234= NC_000001.10:g.817234A>C NC_000001.10:g.817234A>G NC_000001.10:g.817234A>T
Help

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#.

61 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6879529 Feb 20, 2003 (111)
2 SC_SNP ss16312893 Feb 27, 2004 (120)
3 SSAHASNP ss22883191 Apr 05, 2004 (121)
4 PERLEGEN ss24214987 Sep 20, 2004 (124)
5 ABI ss41238922 Mar 14, 2006 (126)
6 HGSV ss78850786 Dec 07, 2007 (129)
7 HGSV ss82689427 Dec 15, 2007 (130)
8 HGSV ss84949990 Dec 15, 2007 (130)
9 HGSV ss85107385 Dec 15, 2007 (130)
10 BCMHGSC_JDW ss87156321 Mar 23, 2008 (129)
11 HUMANGENOME_JCVI ss97913295 Feb 05, 2009 (130)
12 BGI ss105111775 Dec 01, 2009 (131)
13 1000GENOMES ss107938306 Jan 22, 2009 (130)
14 1000GENOMES ss109937503 Jan 24, 2009 (130)
15 ILLUMINA-UK ss118438541 Feb 14, 2009 (130)
16 ENSEMBL ss137752577 Dec 01, 2009 (131)
17 ENSEMBL ss138884520 Dec 01, 2009 (131)
18 GMI ss154522854 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss162980960 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss205458740 Jul 04, 2010 (132)
21 1000GENOMES ss218190619 Jul 14, 2010 (132)
22 1000GENOMES ss230395613 Jul 14, 2010 (132)
23 1000GENOMES ss238115129 Jul 15, 2010 (132)
24 BL ss252864465 May 09, 2011 (134)
25 GMI ss275681168 May 04, 2012 (137)
26 GMI ss283987517 Apr 25, 2013 (138)
27 PJP ss290493863 May 09, 2011 (134)
28 SSMP ss647516647 Apr 25, 2013 (138)
29 EVA-GONL ss974769770 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1067612487 Aug 21, 2014 (142)
31 1000GENOMES ss1289340795 Aug 21, 2014 (142)
32 DDI ss1425685041 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1573851259 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1599378675 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1642372708 Apr 01, 2015 (144)
36 WEILL_CORNELL_DGM ss1917961047 Feb 12, 2016 (147)
37 JJLAB ss2019498552 Sep 14, 2016 (149)
38 USC_VALOUEV ss2147484682 Dec 20, 2016 (150)
39 TOPMED ss2321506081 Dec 20, 2016 (150)
40 GRF ss2697375222 Nov 08, 2017 (151)
41 GNOMAD ss2750643647 Nov 08, 2017 (151)
42 SWEGEN ss2986149936 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023513748 Nov 08, 2017 (151)
44 TOPMED ss3066409965 Nov 08, 2017 (151)
45 TOPMED ss3066409966 Nov 08, 2017 (151)
46 CSHL ss3343272885 Nov 08, 2017 (151)
47 URBANLAB ss3646581310 Oct 11, 2018 (152)
48 EVA_DECODE ss3685992751 Jul 12, 2019 (153)
49 ACPOP ss3726716621 Jul 12, 2019 (153)
50 EVA ss3745721347 Jul 12, 2019 (153)
51 PACBIO ss3783302356 Jul 12, 2019 (153)
52 PACBIO ss3788980109 Jul 12, 2019 (153)
53 PACBIO ss3793852670 Jul 12, 2019 (153)
54 KHV_HUMAN_GENOMES ss3798744051 Jul 12, 2019 (153)
55 EVA ss3825981560 Apr 25, 2020 (154)
56 EVA ss3836378498 Apr 25, 2020 (154)
57 EVA ss3841782507 Apr 25, 2020 (154)
58 SGDP_PRJ ss3847996898 Apr 25, 2020 (154)
59 KRGDB ss3892837515 Apr 25, 2020 (154)
60 TOPMED ss4436444022 Apr 25, 2021 (155)
61 TOMMO_GENOMICS ss5142054541 Apr 25, 2021 (155)
62 1000Genomes NC_000001.10 - 817234 Oct 11, 2018 (152)
63 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 817234 Oct 11, 2018 (152)
64 The Danish reference pan genome NC_000001.10 - 817234 Apr 25, 2020 (154)
65 gnomAD - Genomes NC_000001.11 - 881854 Apr 25, 2021 (155)
66 Genome of the Netherlands Release 5 NC_000001.10 - 817234 Apr 25, 2020 (154)
67 KOREAN population from KRGDB NC_000001.10 - 817234 Apr 25, 2020 (154)
68 Northern Sweden NC_000001.10 - 817234 Jul 12, 2019 (153)
69 Qatari NC_000001.10 - 817234 Apr 25, 2020 (154)
70 SGDP_PRJ NC_000001.10 - 817234 Apr 25, 2020 (154)
71 Siberian NC_000001.10 - 817234 Apr 25, 2020 (154)
72 8.3KJPN NC_000001.10 - 817234 Apr 25, 2021 (155)
73 TopMed NC_000001.11 - 881854 Apr 25, 2021 (155)
74 UK 10K study - Twins NC_000001.10 - 817234 Oct 11, 2018 (152)
75 A Vietnamese Genetic Variation Database NC_000001.10 - 817234 Jul 12, 2019 (153)
76 ALFA NC_000001.11 - 881854 Apr 25, 2021 (155)
Help

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)
rs17836726 Dec 02, 2004 (124)
rs58485525 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
14909, ss3892837515 NC_000001.10:817233:A:C NC_000001.11:881853:A:C (self)
3394525417, ss3066409965 NC_000001.11:881853:A:G NC_000001.11:881853:A:G (self)
ss78850786, ss82689427, ss84949990, ss85107385 NC_000001.8:857096:A:T NC_000001.11:881853:A:T (self)
ss87156321, ss107938306, ss109937503, ss118438541, ss162980960, ss205458740, ss252864465, ss275681168, ss283987517, ss290493863 NC_000001.9:807096:A:T NC_000001.11:881853:A:T (self)
5584, 666, 1358493, 743, 14909, 1486, 2977, 13878, 1036, 23848, 666, 138, ss218190619, ss230395613, ss238115129, ss647516647, ss974769770, ss1067612487, ss1289340795, ss1425685041, ss1573851259, ss1599378675, ss1642372708, ss1917961047, ss2019498552, ss2147484682, ss2321506081, ss2697375222, ss2750643647, ss2986149936, ss3343272885, ss3726716621, ss3745721347, ss3783302356, ss3788980109, ss3793852670, ss3825981560, ss3836378498, ss3847996898, ss3892837515, ss5142054541 NC_000001.10:817233:A:T NC_000001.11:881853:A:T (self)
74889, 23740, 50357, 3394525417, ss3023513748, ss3066409966, ss3646581310, ss3685992751, ss3798744051, ss3841782507, ss4436444022 NC_000001.11:881853:A:T NC_000001.11:881853:A:T (self)
ss6879529, ss22883191, ss24214987, ss41238922, ss97913295, ss105111775, ss137752577, ss138884520, ss154522854 NT_004350.19:295865:A:T NC_000001.11:881853:A:T (self)
ss16312893 NT_079624.1:7474:A:T NC_000001.11:881853:A:T (self)
Help

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

No publications for rs4970387

Help

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.

Software version is: 2.0.1.post596+ae089ad