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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.

rs12353938

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:30375581 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.016995 (2359/138806, GnomAD)
T=0.00718 (169/23548, ALFA)
T=0.014 (3/216, Qatari) (+ 1 more)
C=0.42 (5/12, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 23548 C=0.99282 T=0.00718
European Sub 18206 C=0.99995 T=0.00005
African Sub 3074 C=0.9506 T=0.0494
African Others Sub 118 C=0.966 T=0.034
African American Sub 2956 C=0.9499 T=0.0501
Asian Sub 124 C=1.000 T=0.000
East Asian Sub 98 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 168 C=0.976 T=0.024
Latin American 2 Sub 700 C=0.994 T=0.006
South Asian Sub 110 C=1.000 T=0.000
Other Sub 1166 C=0.9931 T=0.0069


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 138806 C=0.983005 T=0.016995
gnomAD - Genomes European Sub 75556 C=0.99987 T=0.00013
gnomAD - Genomes African Sub 41152 C=0.94498 T=0.05502
gnomAD - Genomes American Sub 13558 C=0.99587 T=0.00413
gnomAD - Genomes Ashkenazi Jewish Sub 3306 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3102 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2132 C=0.9864 T=0.0136
Allele Frequency Aggregator Total Global 23548 C=0.99282 T=0.00718
Allele Frequency Aggregator European Sub 18206 C=0.99995 T=0.00005
Allele Frequency Aggregator African Sub 3074 C=0.9506 T=0.0494
Allele Frequency Aggregator Other Sub 1166 C=0.9931 T=0.0069
Allele Frequency Aggregator Latin American 2 Sub 700 C=0.994 T=0.006
Allele Frequency Aggregator Latin American 1 Sub 168 C=0.976 T=0.024
Allele Frequency Aggregator Asian Sub 124 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 110 C=1.000 T=0.000
Qatari Global Study-wide 216 C=0.986 T=0.014
SGDP_PRJ Global Study-wide 12 C=0.42 T=0.58
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.30375581C>T
GRCh37.p13 chr 1 NC_000001.10:g.30848428C>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
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 C= T
GRCh38.p14 chr 1 NC_000001.11:g.30375581= NC_000001.11:g.30375581C>T
GRCh37.p13 chr 1 NC_000001.10:g.30848428= NC_000001.10:g.30848428C>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#.

21 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18857945 Feb 28, 2004 (120)
2 1000GENOMES ss328506303 May 09, 2011 (134)
3 ILLUMINA ss480923787 May 04, 2012 (137)
4 ILLUMINA ss482312735 May 04, 2012 (137)
5 ILLUMINA ss534026606 Sep 08, 2015 (146)
6 ILLUMINA ss779456585 Sep 08, 2015 (146)
7 ILLUMINA ss781352422 Sep 08, 2015 (146)
8 ILLUMINA ss834926252 Sep 08, 2015 (146)
9 WEILL_CORNELL_DGM ss1918206159 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2161120988 Dec 20, 2016 (150)
11 ILLUMINA ss2632495759 Nov 08, 2017 (151)
12 GNOMAD ss2753232314 Nov 08, 2017 (151)
13 ILLUMINA ss3626059614 Oct 11, 2018 (152)
14 ILLUMINA ss3630532971 Oct 11, 2018 (152)
15 EVA_DECODE ss3686442987 Jul 12, 2019 (153)
16 SGDP_PRJ ss3848508816 Apr 25, 2020 (154)
17 1000G_HIGH_COVERAGE ss5241683063 Oct 13, 2022 (156)
18 EVA ss5317652799 Oct 13, 2022 (156)
19 SANFORD_IMAGENETICS ss5625205904 Oct 13, 2022 (156)
20 EVA ss5907589471 Oct 13, 2022 (156)
21 EVA ss5937023178 Oct 13, 2022 (156)
22 gnomAD - Genomes NC_000001.11 - 30375581 Apr 25, 2021 (155)
23 Qatari NC_000001.10 - 30848428 Apr 25, 2020 (154)
24 SGDP_PRJ NC_000001.10 - 30848428 Apr 25, 2020 (154)
25 ALFA NC_000001.11 - 30375581 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
ss482312735 NC_000001.9:30621014:C:T NC_000001.11:30375580:C:T (self)
248089, 525796, ss328506303, ss480923787, ss534026606, ss779456585, ss781352422, ss834926252, ss1918206159, ss2632495759, ss2753232314, ss3626059614, ss3630532971, ss3848508816, ss5317652799, ss5625205904, ss5937023178 NC_000001.10:30848427:C:T NC_000001.11:30375580:C:T (self)
6486741, 7176776376, ss2161120988, ss3686442987, ss5241683063, ss5907589471 NC_000001.11:30375580:C:T NC_000001.11:30375580:C:T (self)
ss18857945 NT_004511.16:786828:C:T NC_000001.11:30375580:C: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 rs12353938

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