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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.

rs2907079

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:63792 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00011 (7/65700, GnomAD)
T=0.11115 (1753/15772, 8.3KJPN)
A=0.0000 (0/7394, ALFA) (+ 4 more)
T=0.0000 (0/7394, ALFA)
T=0.0728 (204/2804, KOREAN)
T=0.0191 (33/1724, Korea1K)
G=0.00 (0/16, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OR4F5 : 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.63792G>A
GRCh38.p13 chr 1 NC_000001.11:g.63792G>T
GRCh37.p13 chr 1 NC_000001.10:g.63792G>A
GRCh37.p13 chr 1 NC_000001.10:g.63792G>T
OR4G11P pseudogene NG_004423.3:g.877G>A
OR4G11P pseudogene NG_004423.3:g.877G>T
Gene: OR4F5, olfactory receptor family 4 subfamily F member 5 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
OR4F5 transcript NM_001005484.2:c. 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 7394 G=1.0000 A=0.0000, T=0.0000
European Sub 4744 G=1.0000 A=0.0000, T=0.0000
African Sub 1730 G=1.0000 A=0.0000, T=0.0000
African Others Sub 64 G=1.00 A=0.00, T=0.00
African American Sub 1666 G=1.0000 A=0.0000, T=0.0000
Asian Sub 104 G=1.000 A=0.000, T=0.000
East Asian Sub 80 G=1.00 A=0.00, T=0.00
Other Asian Sub 24 G=1.00 A=0.00, T=0.00
Latin American 1 Sub 94 G=1.00 A=0.00, T=0.00
Latin American 2 Sub 360 G=1.000 A=0.000, T=0.000
South Asian Sub 74 G=1.00 A=0.00, T=0.00
Other Sub 288 G=1.000 A=0.000, T=0.000


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 65700 G=0.99989 A=0.00011
gnomAD - Genomes European Sub 32474 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 22836 G=0.99974 A=0.00026
gnomAD - Genomes American Sub 5632 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 2652 G=1.0000 A=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 1158 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 948 G=0.999 A=0.001
8.3KJPN JAPANESE Study-wide 15772 G=0.88885 T=0.11115
KOREAN population from KRGDB KOREAN Study-wide 2804 G=0.9272 T=0.0728
Korean Genome Project KOREAN Study-wide 1724 G=0.9809 T=0.0191
SGDP_PRJ Global Study-wide 16 G=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 G= A T
GRCh38.p13 chr 1 NC_000001.11:g.63792= NC_000001.11:g.63792G>A NC_000001.11:g.63792G>T
GRCh37.p13 chr 1 NC_000001.10:g.63792= NC_000001.10:g.63792G>A NC_000001.10:g.63792G>T
OR4G11P pseudogene NG_004423.3:g.877= NG_004423.3:g.877G>A NG_004423.3:g.877G>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#.

18 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2224027 Oct 08, 2002 (108)
2 SC_JCM ss4102161 Nov 05, 2001 (101)
3 BCMHGSC_JDW ss87153283 Mar 25, 2008 (130)
4 ILLUMINA ss160597909 Dec 01, 2009 (131)
5 ENSEMBL ss161259461 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss162980565 Jul 04, 2010 (132)
7 ILLUMINA ss481606063 Sep 08, 2015 (146)
8 DDI ss1425684561 Apr 01, 2015 (144)
9 HAMMER_LAB ss1793705108 Sep 08, 2015 (146)
10 GNOMAD ss2750604479 Nov 08, 2017 (151)
11 SWEGEN ss2986142053 Nov 08, 2017 (151)
12 TOPMED ss3066322505 Nov 08, 2017 (151)
13 TOPMED ss3066322506 Nov 08, 2017 (151)
14 ILLUMINA ss3635978557 Oct 11, 2018 (152)
15 SGDP_PRJ ss3847984133 Apr 25, 2020 (154)
16 KRGDB ss3892823953 Apr 25, 2020 (154)
17 KOGIC ss3943622693 Apr 25, 2020 (154)
18 TOMMO_GENOMICS ss5142033029 Apr 25, 2021 (155)
19 gnomAD - Genomes NC_000001.11 - 63792 Apr 25, 2021 (155)
20 KOREAN population from KRGDB NC_000001.10 - 63792 Apr 25, 2020 (154)
21 Korean Genome Project NC_000001.11 - 63792 Apr 25, 2020 (154)
22 SGDP_PRJ NC_000001.10 - 63792 Apr 25, 2020 (154)
23 8.3KJPN NC_000001.10 - 63792 Apr 25, 2021 (155)
24 ALFA NC_000001.11 - 63792 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)
rs62639103 May 26, 2008 (130)
rs756694002 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2750604479 NC_000001.10:63791:G:A NC_000001.11:63791:G:A (self)
5465, 15073998866, ss3066322505 NC_000001.11:63791:G:A NC_000001.11:63791:G:A (self)
ss87153283, ss162980565 NC_000001.9:53654:G:T NC_000001.11:63791:G:T (self)
1347, 1113, 2336, ss481606063, ss1425684561, ss1793705108, ss2750604479, ss2986142053, ss3635978557, ss3847984133, ss3892823953, ss5142033029 NC_000001.10:63791:G:T NC_000001.11:63791:G:T (self)
694, 15073998866, ss3066322506, ss3943622693 NC_000001.11:63791:G:T NC_000001.11:63791:G:T (self)
ss2224027, ss4102161, ss160597909, ss161259461 NT_077402.2:53791:G:T NC_000001.11:63791:G: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 rs2907079

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