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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:36313972 (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.

Variation Type
SNV Single Nucleotide Variation
T=0.02528 (884/34962, GnomAD)
T=0.00809 (96/11862, ALFA)
T=0.0481 (140/2908, KOREAN) (+ 6 more)
C=0.500 (108/216, Qatari)
T=0.500 (108/216, Qatari)
C=0.50 (11/22, SGDP_PRJ)
T=0.50 (11/22, SGDP_PRJ)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SH3D21 : Intron Variant
0 citations
Genomic View
See rs on genome

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.36313972C>T
GRCh37.p13 chr 1 NC_000001.10:g.36779573C>T
Gene: SH3D21, SH3 domain containing 21 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SH3D21 transcript variant 1 NM_001162530.2:c.769+4382…


N/A Intron Variant
SH3D21 transcript variant 2 NM_024676.5:c.436+4382C>T N/A Intron Variant
SH3D21 transcript variant X7 XM_011542153.2:c.769+4382…


N/A Intron Variant
SH3D21 transcript variant X1 XM_017002340.1:c.769+4382…


N/A Intron Variant
SH3D21 transcript variant X2 XM_017002341.1:c.769+4382…


N/A Intron Variant
SH3D21 transcript variant X3 XM_017002342.2:c.769+4382…


N/A Intron Variant
SH3D21 transcript variant X4 XM_017002343.1:c.769+4382…


N/A Intron Variant
SH3D21 transcript variant X5 XM_017002344.1:c.769+4382…


N/A Intron Variant
SH3D21 transcript variant X6 XM_017002345.1:c.769+4382…


N/A Intron Variant
SH3D21 transcript variant X8 XM_017002346.1:c.-52+4382…


N/A Intron Variant

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
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 11862 C=0.99191 T=0.00809
European Sub 7618 C=0.9954 T=0.0046
African Sub 2816 C=0.9819 T=0.0181
African Others Sub 108 C=0.991 T=0.009
African American Sub 2708 C=0.9815 T=0.0185
Asian Sub 108 C=0.991 T=0.009
East Asian Sub 84 C=1.00 T=0.00
Other Asian Sub 24 C=0.96 T=0.04
Latin American 1 Sub 146 C=0.986 T=0.014
Latin American 2 Sub 610 C=0.992 T=0.008
South Asian Sub 94 C=1.00 T=0.00
Other Sub 470 C=0.996 T=0.004


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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 34962 C=0.97472 T=0.02528
gnomAD - Genomes European Sub 17892 C=0.97166 T=0.02834
gnomAD - Genomes African Sub 13340 C=0.97834 T=0.02166
gnomAD - Genomes American Sub 1410 C=0.9745 T=0.0255
gnomAD - Genomes Ashkenazi Jewish Sub 1280 C=0.9781 T=0.0219
gnomAD - Genomes East Asian Sub 636 C=0.972 T=0.028
gnomAD - Genomes Other Sub 404 C=0.985 T=0.015
Allele Frequency Aggregator Total Global 11862 C=0.99191 T=0.00809
Allele Frequency Aggregator European Sub 7618 C=0.9954 T=0.0046
Allele Frequency Aggregator African Sub 2816 C=0.9819 T=0.0181
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.992 T=0.008
Allele Frequency Aggregator Other Sub 470 C=0.996 T=0.004
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.986 T=0.014
Allele Frequency Aggregator Asian Sub 108 C=0.991 T=0.009
Allele Frequency Aggregator South Asian Sub 94 C=1.00 T=0.00
KOREAN population from KRGDB KOREAN Study-wide 2908 C=0.9519 T=0.0481
Qatari Global Study-wide 216 C=0.500 T=0.500
SGDP_PRJ Global Study-wide 22 C=0.50 T=0.50
Siberian Global Study-wide 4 C=0.5 T=0.5

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.p13 chr 1 NC_000001.11:g.36313972= NC_000001.11:g.36313972C>T
GRCh37.p13 chr 1 NC_000001.10:g.36779573= NC_000001.10:g.36779573C>T
SH3D21 transcript variant 1 NM_001162530.1:c.769+4382= NM_001162530.1:c.769+4382C>T
SH3D21 transcript variant 1 NM_001162530.2:c.769+4382= NM_001162530.2:c.769+4382C>T
SH3D21 transcript variant 2 NM_024676.4:c.436+4382= NM_024676.4:c.436+4382C>T
SH3D21 transcript variant 2 NM_024676.5:c.436+4382= NM_024676.5:c.436+4382C>T
SH3D21 transcript variant X1 XM_005271204.1:c.769+4382= XM_005271204.1:c.769+4382C>T
SH3D21 transcript variant X2 XM_005271205.1:c.160+4382= XM_005271205.1:c.160+4382C>T
SH3D21 transcript variant X4 XM_005271207.1:c.-146+4382= XM_005271207.1:c.-146+4382C>T
SH3D21 transcript variant X7 XM_011542153.2:c.769+4382= XM_011542153.2:c.769+4382C>T
SH3D21 transcript variant X1 XM_017002340.1:c.769+4382= XM_017002340.1:c.769+4382C>T
SH3D21 transcript variant X2 XM_017002341.1:c.769+4382= XM_017002341.1:c.769+4382C>T
SH3D21 transcript variant X3 XM_017002342.2:c.769+4382= XM_017002342.2:c.769+4382C>T
SH3D21 transcript variant X4 XM_017002343.1:c.769+4382= XM_017002343.1:c.769+4382C>T
SH3D21 transcript variant X5 XM_017002344.1:c.769+4382= XM_017002344.1:c.769+4382C>T
SH3D21 transcript variant X6 XM_017002345.1:c.769+4382= XM_017002345.1:c.769+4382C>T
SH3D21 transcript variant X8 XM_017002346.1:c.-52+4382= XM_017002346.1:c.-52+4382C>T

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#.

13 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16401534 Feb 27, 2004 (120)
2 SC_SNP ss18081643 Feb 27, 2004 (120)
3 SC_SNP ss19058871 Feb 27, 2004 (120)
4 BGI ss102733945 Dec 01, 2009 (131)
5 WEILL_CORNELL_DGM ss1918245996 Feb 12, 2016 (147)
6 USC_VALOUEV ss2147645538 Dec 20, 2016 (150)
7 GRF ss2697553437 Nov 08, 2017 (151)
8 SWEGEN ss2986612311 Nov 08, 2017 (151)
9 TOPMED ss3073322890 Nov 08, 2017 (151)
10 CSHL ss3343402720 Nov 08, 2017 (151)
11 SGDP_PRJ ss3848591863 Apr 25, 2020 (154)
12 KRGDB ss3893550260 Apr 25, 2020 (154)
13 GNOMAD ss3991440098 Apr 25, 2021 (155)
14 gnomAD - Genomes NC_000001.11 - 36313972 Apr 25, 2021 (155)
15 KOREAN population from KRGDB NC_000001.10 - 36779573 Apr 25, 2020 (154)
16 Qatari NC_000001.10 - 36779573 Apr 25, 2020 (154)
17 SGDP_PRJ NC_000001.10 - 36779573 Apr 25, 2020 (154)
18 Siberian NC_000001.10 - 36779573 Apr 25, 2020 (154)
19 ALFA NC_000001.11 - 36313972 Apr 25, 2021 (155)

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
727654, 287926, 608843, 161892, ss1918245996, ss2147645538, ss2697553437, ss2986612311, ss3343402720, ss3848591863, ss3893550260 NC_000001.10:36779572:C:T NC_000001.11:36313971:C:T (self)
7698664, 1431102229, ss3073322890, ss3991440098 NC_000001.11:36313971:C:T NC_000001.11:36313971:C:T (self)
ss19058871, ss102733945 NT_032977.9:6751490:C:T NC_000001.11:36313971:C:T (self)
ss16401534, ss18081643 NT_079482.1:1481318:C:T NC_000001.11:36313971:C:T (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs10908296


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