Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

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.

rs368517397

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:629661 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000596 (76/127540, GnomAD)
A=0.00012 (3/25538, 14KJPN)
A=0.00061 (10/16312, ALFA) (+ 4 more)
A=0.00007 (1/15274, 8.3KJPN)
A=0.0016 (10/6404, 1000G_30x)
A=0.0034 (17/5008, 1000G)
A=0.0044 (8/1802, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC101928626 : 2KB Upstream Variant
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 16312 G=0.99939 A=0.00061
European Sub 12060 G=0.99975 A=0.00025
African Sub 2816 G=0.9989 A=0.0011
African Others Sub 108 G=1.000 A=0.000
African American Sub 2708 G=0.9989 A=0.0011
Asian Sub 108 G=0.991 A=0.009
East Asian Sub 84 G=0.99 A=0.01
Other Asian Sub 24 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 94 G=1.00 A=0.00
Other Sub 478 G=0.994 A=0.006


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 127540 G=0.999404 A=0.000596
gnomAD - Genomes European Sub 72370 G=0.99983 A=0.00017
gnomAD - Genomes African Sub 34622 G=0.99887 A=0.00113
gnomAD - Genomes American Sub 12618 G=0.99992 A=0.00008
gnomAD - Genomes Ashkenazi Jewish Sub 3110 G=0.9968 A=0.0032
gnomAD - Genomes East Asian Sub 2892 G=0.9962 A=0.0038
gnomAD - Genomes Other Sub 1928 G=0.9984 A=0.0016
14KJPN JAPANESE Study-wide 25538 G=0.99988 A=0.00012
Allele Frequency Aggregator Total Global 16312 G=0.99939 A=0.00061
Allele Frequency Aggregator European Sub 12060 G=0.99975 A=0.00025
Allele Frequency Aggregator African Sub 2816 G=0.9989 A=0.0011
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 478 G=0.994 A=0.006
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 G=0.991 A=0.009
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00
8.3KJPN JAPANESE Study-wide 15274 G=0.99993 A=0.00007
1000Genomes_30x Global Study-wide 6404 G=0.9984 A=0.0016
1000Genomes_30x African Sub 1786 G=0.9972 A=0.0028
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=0.9975 A=0.0025
1000Genomes_30x East Asian Sub 1170 G=0.9983 A=0.0017
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9966 A=0.0034
1000Genomes African Sub 1322 G=0.9977 A=0.0023
1000Genomes East Asian Sub 1008 G=0.9921 A=0.0079
1000Genomes Europe Sub 1006 G=0.9950 A=0.0050
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=1.000 A=0.000
Korean Genome Project KOREAN Study-wide 1802 G=0.9956 A=0.0044
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.p14 chr 1 NC_000001.11:g.629661G>A
GRCh37.p13 chr 1 NC_000001.10:g.565041G>A
MTND2P28 pseudogene NG_032768.1:g.122G>A
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
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
GRCh38.p14 chr 1 NC_000001.11:g.629661= NC_000001.11:g.629661G>A
GRCh37.p13 chr 1 NC_000001.10:g.565041= NC_000001.10:g.565041G>A
MTND2P28 pseudogene NG_032768.1:g.122= NG_032768.1:g.122G>A
MTND2 transcript NM_173709.1:c.22= NM_173709.1:c.22G>A
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#.

12 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 TISHKOFF ss553710101 Apr 25, 2013 (138)
2 1000GENOMES ss1289336897 Aug 21, 2014 (142)
3 GNOMAD ss2750622561 Nov 08, 2017 (151)
4 KHV_HUMAN_GENOMES ss3798742792 Jul 12, 2019 (153)
5 KOGIC ss3943626536 Apr 25, 2020 (154)
6 TOMMO_GENOMICS ss5142044151 Apr 25, 2021 (155)
7 1000G_HIGH_COVERAGE ss5240859611 Oct 12, 2022 (156)
8 EVA ss5316177165 Oct 12, 2022 (156)
9 1000G_HIGH_COVERAGE ss5512482725 Oct 12, 2022 (156)
10 SANFORD_IMAGENETICS ss5624746048 Oct 12, 2022 (156)
11 TOMMO_GENOMICS ss5666181560 Oct 12, 2022 (156)
12 YY_MCH ss5800242376 Oct 12, 2022 (156)
13 1000Genomes NC_000001.10 - 565041 Oct 11, 2018 (152)
14 1000Genomes_30x NC_000001.11 - 629661 Oct 12, 2022 (156)
15 gnomAD - Genomes NC_000001.11 - 629661 Apr 25, 2021 (155)
16 Korean Genome Project NC_000001.11 - 629661 Apr 25, 2020 (154)
17 8.3KJPN NC_000001.10 - 565041 Apr 25, 2021 (155)
18 14KJPN NC_000001.11 - 629661 Oct 12, 2022 (156)
19 ALFA NC_000001.11 - 629661 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1531, 13458, ss553710101, ss1289336897, ss2750622561, ss5142044151, ss5316177165, ss5624746048 NC_000001.10:565040:G:A NC_000001.11:629660:G:A (self)
8660, 38064, 4537, 18664, 9277524547, ss3798742792, ss3943626536, ss5240859611, ss5512482725, ss5666181560, ss5800242376 NC_000001.11:629660:G:A NC_000001.11:629660:G:A (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 rs368517397

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.post761+d5e8e07