Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs9701779

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:629994 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.009459 (1205/127388, GnomAD)
G=0.00560 (86/15352, 8.3KJPN)
G=0.00904 (123/13602, ALFA) (+ 4 more)
G=0.0069 (19/2748, KOREAN)
G=0.0303 (55/1818, Korea1K)
G=0.062 (49/792, PRJEB37584)
A=0.00 (0/28, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC101928626 : 2KB Upstream Variant
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.629994A>G
GRCh37.p13 chr 1 NC_000001.10:g.565374A>G
MTND2P28 pseudogene NG_032768.1:g.455A>G
Gene: LOC101928626, uncharacterized LOC101928626 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC101928626 transcript NR_125957.1:n. N/A Upstream Transcript Variant
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 (New)
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 13602 A=0.99096 G=0.00904
European Sub 8838 A=0.9985 G=0.0015
African Sub 2918 A=0.9976 G=0.0024
African Others Sub 112 A=1.000 G=0.000
African American Sub 2806 A=0.9975 G=0.0025
Asian Sub 120 A=1.000 G=0.000
East Asian Sub 94 A=1.00 G=0.00
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 156 A=0.962 G=0.038
Latin American 2 Sub 628 A=0.887 G=0.113
South Asian Sub 94 A=1.00 G=0.00
Other Sub 848 A=0.969 G=0.031


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
gnomAD - Genomes Global Study-wide 127388 A=0.990541 G=0.009459
gnomAD - Genomes European Sub 73546 A=0.99962 G=0.00038
gnomAD - Genomes African Sub 34722 A=0.99816 G=0.00184
gnomAD - Genomes American Sub 10998 A=0.91007 G=0.08993
gnomAD - Genomes Ashkenazi Jewish Sub 3202 A=0.9997 G=0.0003
gnomAD - Genomes East Asian Sub 3000 A=0.9790 G=0.0210
gnomAD - Genomes Other Sub 1920 A=0.9688 G=0.0312
8.3KJPN JAPANESE Study-wide 15352 A=0.99440 G=0.00560
KOREAN population from KRGDB KOREAN Study-wide 2748 A=0.9931 G=0.0069
Korean Genome Project KOREAN Study-wide 1818 A=0.9697 G=0.0303
CNV burdens in cranial meningiomas Global Study-wide 792 A=0.938 G=0.062
CNV burdens in cranial meningiomas CRM Sub 792 A=0.938 G=0.062
SGDP_PRJ Global Study-wide 28 A=0.00 G=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= G
GRCh38.p13 chr 1 NC_000001.11:g.629994= NC_000001.11:g.629994A>G
GRCh37.p13 chr 1 NC_000001.10:g.565374= NC_000001.10:g.565374A>G
MTND2P28 pseudogene NG_032768.1:g.455= NG_032768.1:g.455A>G
MTND2 transcript NM_173709.1:c.355= NM_173709.1:c.355A>G
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#.

27 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss13505191 Dec 05, 2003 (119)
2 BROAD ss37044387 May 24, 2005 (131)
3 ILLUMINA ss66863449 Dec 02, 2006 (131)
4 ILLUMINA ss66931988 Dec 02, 2006 (131)
5 ILLUMINA ss68074757 Dec 12, 2006 (131)
6 PERLEGEN ss69268945 May 18, 2007 (131)
7 ILLUMINA ss70458809 May 26, 2008 (131)
8 ILLUMINA ss70979349 May 18, 2007 (131)
9 ILLUMINA ss75877932 Dec 07, 2007 (131)
10 ILLUMINA ss152536650 Dec 01, 2009 (131)
11 ILLUMINA ss159102679 Dec 01, 2009 (131)
12 ILLUMINA ss169133891 Jul 04, 2010 (132)
13 GMI ss275680272 May 04, 2012 (137)
14 ILLUMINA ss537623970 Sep 08, 2015 (146)
15 ILLUMINA ss778717296 Sep 08, 2015 (146)
16 ILLUMINA ss834176613 Sep 08, 2015 (146)
17 EVA ss2137544097 Apr 25, 2021 (155)
18 ILLUMINA ss2632465436 Nov 08, 2017 (151)
19 GRF ss2697373716 Nov 08, 2017 (151)
20 GNOMAD ss2750622665 Nov 08, 2017 (151)
21 TOPMED ss3066366855 Nov 08, 2017 (151)
22 ILLUMINA ss3626006462 Oct 11, 2018 (152)
23 ILLUMINA ss3630505563 Oct 11, 2018 (152)
24 SGDP_PRJ ss3847990432 Apr 25, 2020 (154)
25 KRGDB ss3892830320 Apr 25, 2020 (154)
26 KOGIC ss3943626561 Apr 25, 2020 (154)
27 TOMMO_GENOMICS ss5142044184 Apr 25, 2021 (155)
28 gnomAD - Genomes NC_000001.11 - 629994 Apr 25, 2021 (155)
29 KOREAN population from KRGDB NC_000001.10 - 565374 Apr 25, 2020 (154)
30 Korean Genome Project NC_000001.11 - 629994 Apr 25, 2020 (154)
31 CNV burdens in cranial meningiomas NC_000001.10 - 565374 Apr 25, 2021 (155)
32 SGDP_PRJ NC_000001.10 - 565374 Apr 25, 2020 (154)
33 8.3KJPN NC_000001.10 - 565374 Apr 25, 2021 (155)
34 ALFA NC_000001.11 - 629994 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)
rs28357978 Dec 02, 2009 (131)
rs41557914 May 26, 2008 (130)
rs45594535 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss275680272 NC_000001.9:555236:A:G NC_000001.11:629993:A:G (self)
7714, 1, 7412, 13491, ss537623970, ss778717296, ss834176613, ss2137544097, ss2632465436, ss2697373716, ss2750622665, ss3626006462, ss3630505563, ss3847990432, ss3892830320, ss5142044184 NC_000001.10:565373:A:G NC_000001.11:629993:A:G (self)
38161, 4562, 9363075976, ss3066366855, ss3943626561 NC_000001.11:629993:A:G NC_000001.11:629993:A:G (self)
ss37044387, ss66863449, ss66931988, ss68074757, ss69268945, ss70458809, ss70979349, ss75877932, ss152536650, ss159102679, ss169133891 NT_004350.19:44005:A:G NC_000001.11:629993:A:G (self)
ss13505191 NT_034471.3:44005:A:G NC_000001.11:629993:A:G (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 rs9701779

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