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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.

rs28402963

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:62203 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.40144 (38757/96546, GnomAD)
C=0.12791 (2120/16574, 8.3KJPN)
C=0.48448 (7833/16168, ALFA) (+ 4 more)
C=0.1240 (357/2878, KOREAN)
C=0.1108 (201/1814, Korea1K)
T=0.395 (116/294, SGDP_PRJ)
C=0.476 (98/206, Qatari)
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.62203T>C
GRCh38.p13 chr 1 NC_000001.11:g.62203T>G
GRCh37.p13 chr 1 NC_000001.10:g.62203T>C
GRCh37.p13 chr 1 NC_000001.10:g.62203T>G
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 16168 T=0.51552 C=0.48448
European Sub 11918 T=0.45931 C=0.54069
African Sub 2816 T=0.6989 C=0.3011
African Others Sub 108 T=0.667 C=0.333
African American Sub 2708 T=0.7001 C=0.2999
Asian Sub 108 T=0.843 C=0.157
East Asian Sub 84 T=0.85 C=0.15
Other Asian Sub 24 T=0.83 C=0.17
Latin American 1 Sub 146 T=0.568 C=0.432
Latin American 2 Sub 610 T=0.628 C=0.372
South Asian Sub 94 T=0.59 C=0.41
Other Sub 476 T=0.590 C=0.410


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 96546 T=0.59856 C=0.40144
gnomAD - Genomes European Sub 53058 T=0.51466 C=0.48534
gnomAD - Genomes African Sub 27914 T=0.71860 C=0.28140
gnomAD - Genomes American Sub 9266 T=0.6444 C=0.3556
gnomAD - Genomes East Asian Sub 2534 T=0.9380 C=0.0620
gnomAD - Genomes Ashkenazi Jewish Sub 2332 T=0.5069 C=0.4931
gnomAD - Genomes Other Sub 1442 T=0.6193 C=0.3807
8.3KJPN JAPANESE Study-wide 16574 T=0.87209 C=0.12791
KOREAN population from KRGDB KOREAN Study-wide 2878 T=0.8760 C=0.1240, G=0.0000
Korean Genome Project KOREAN Study-wide 1814 T=0.8892 C=0.1108
SGDP_PRJ Global Study-wide 294 T=0.395 C=0.605
Qatari Global Study-wide 206 T=0.524 C=0.476
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 T= C G
GRCh38.p13 chr 1 NC_000001.11:g.62203= NC_000001.11:g.62203T>C NC_000001.11:g.62203T>G
GRCh37.p13 chr 1 NC_000001.10:g.62203= NC_000001.10:g.62203T>C NC_000001.10:g.62203T>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#.

21 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35129783 May 24, 2005 (125)
2 1000GENOMES ss107938256 Jan 22, 2009 (130)
3 BL ss252863954 May 09, 2011 (134)
4 GMI ss275679917 May 04, 2012 (137)
5 SSMP ss647514835 Apr 25, 2013 (138)
6 DDI ss1425684557 Apr 01, 2015 (144)
7 HAMMER_LAB ss1793705099 Sep 08, 2015 (146)
8 WEILL_CORNELL_DGM ss1917958271 Feb 12, 2016 (147)
9 ILLUMINA ss1958229892 Feb 12, 2016 (147)
10 GRF ss2697373012 Nov 08, 2017 (151)
11 GNOMAD ss2750604306 Nov 08, 2017 (151)
12 SWEGEN ss2986142019 Nov 08, 2017 (151)
13 ILLUMINA ss3021042933 Nov 08, 2017 (151)
14 TOPMED ss3066322118 Nov 08, 2017 (151)
15 CSHL ss3343271557 Nov 08, 2017 (151)
16 URBANLAB ss3646580393 Oct 11, 2018 (152)
17 ILLUMINA ss3651364992 Oct 11, 2018 (152)
18 SGDP_PRJ ss3847984082 Apr 25, 2020 (154)
19 KRGDB ss3892823913 Apr 25, 2020 (154)
20 KOGIC ss3943622663 Apr 25, 2020 (154)
21 TOMMO_GENOMICS ss5142032938 Apr 25, 2021 (155)
22 gnomAD - Genomes NC_000001.11 - 62203 Apr 25, 2021 (155)
23 KOREAN population from KRGDB NC_000001.10 - 62203 Apr 25, 2020 (154)
24 Korean Genome Project NC_000001.11 - 62203 Apr 25, 2020 (154)
25 Qatari NC_000001.10 - 62203 Apr 25, 2020 (154)
26 SGDP_PRJ NC_000001.10 - 62203 Apr 25, 2020 (154)
27 8.3KJPN NC_000001.10 - 62203 Apr 25, 2021 (155)
28 ALFA NC_000001.11 - 62203 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
ss35129783 NC_000001.8:52065:T:C NC_000001.11:62202:T:C (self)
ss107938256, ss252863954, ss275679917 NC_000001.9:52065:T:C NC_000001.11:62202:T:C (self)
1307, 201, 1062, 2245, ss647514835, ss1425684557, ss1793705099, ss1917958271, ss1958229892, ss2697373012, ss2750604306, ss2986142019, ss3021042933, ss3343271557, ss3651364992, ss3847984082, ss3892823913, ss5142032938 NC_000001.10:62202:T:C NC_000001.11:62202:T:C (self)
5145, 664, 2875306719, ss3066322118, ss3646580393, ss3943622663 NC_000001.11:62202:T:C NC_000001.11:62202:T:C (self)
1307, ss3892823913 NC_000001.10:62202:T:G NC_000001.11:62202:T: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 rs28402963

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