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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.

rs781340850

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:23635315 (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>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/251368, GnomAD_exome)
A=0.000007 (1/140224, GnomAD)
T=0.000008 (1/120650, ExAC) (+ 2 more)
A=0.00000 (0/14050, ALFA)
G=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CST3 : Missense 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 14050 C=1.00000 A=0.00000, G=0.00000
European Sub 9690 C=1.0000 A=0.0000, G=0.0000
African Sub 2898 C=1.0000 A=0.0000, G=0.0000
African Others Sub 114 C=1.000 A=0.000, G=0.000
African American Sub 2784 C=1.0000 A=0.0000, G=0.0000
Asian Sub 112 C=1.000 A=0.000, G=0.000
East Asian Sub 86 C=1.00 A=0.00, G=0.00
Other Asian Sub 26 C=1.00 A=0.00, G=0.00
Latin American 1 Sub 146 C=1.000 A=0.000, G=0.000
Latin American 2 Sub 610 C=1.000 A=0.000, G=0.000
South Asian Sub 98 C=1.00 A=0.00, G=0.00
Other Sub 496 C=1.000 A=0.000, G=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 - Exomes Global Study-wide 251368 C=0.999996 T=0.000004
gnomAD - Exomes European Sub 135326 C=0.999993 T=0.000007
gnomAD - Exomes Asian Sub 49006 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34578 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16246 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6138 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140224 C=0.999993 A=0.000007
gnomAD - Genomes European Sub 75938 C=0.99999 A=0.00001
gnomAD - Genomes African Sub 42024 C=1.00000 A=0.00000
gnomAD - Genomes American Sub 13654 C=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 A=0.0000
ExAC Global Study-wide 120650 C=0.999992 T=0.000008
ExAC Europe Sub 72840 C=0.99999 T=0.00001
ExAC Asian Sub 25074 C=1.00000 T=0.00000
ExAC American Sub 11496 C=1.00000 T=0.00000
ExAC African Sub 10342 C=1.00000 T=0.00000
ExAC Other Sub 898 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 14050 C=1.00000 A=0.00000, G=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 A=0.0000, G=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 A=0.0000, G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000, G=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 A=0.000, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000, G=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000, G=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, G=0.00
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 20 NC_000020.11:g.23635315C>A
GRCh38.p14 chr 20 NC_000020.11:g.23635315C>G
GRCh38.p14 chr 20 NC_000020.11:g.23635315C>T
GRCh37.p13 chr 20 NC_000020.10:g.23615952C>A
GRCh37.p13 chr 20 NC_000020.10:g.23615952C>G
GRCh37.p13 chr 20 NC_000020.10:g.23615952C>T
CST3 RefSeqGene NG_012887.3:g.7623G>T
CST3 RefSeqGene NG_012887.3:g.7623G>C
CST3 RefSeqGene NG_012887.3:g.7623G>A
Gene: CST3, cystatin C (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CST3 transcript variant 1 NM_000099.4:c.296G>T C [TGT] > F [TTT] Coding Sequence Variant
cystatin-C precursor NP_000090.1:p.Cys99Phe C (Cys) > F (Phe) Missense Variant
CST3 transcript variant 1 NM_000099.4:c.296G>C C [TGT] > S [TCT] Coding Sequence Variant
cystatin-C precursor NP_000090.1:p.Cys99Ser C (Cys) > S (Ser) Missense Variant
CST3 transcript variant 1 NM_000099.4:c.296G>A C [TGT] > Y [TAT] Coding Sequence Variant
cystatin-C precursor NP_000090.1:p.Cys99Tyr C (Cys) > Y (Tyr) Missense Variant
CST3 transcript variant 2 NM_001288614.2:c.296G>T C [TGT] > F [TTT] Coding Sequence Variant
cystatin-C precursor NP_001275543.1:p.Cys99Phe C (Cys) > F (Phe) Missense Variant
CST3 transcript variant 2 NM_001288614.2:c.296G>C C [TGT] > S [TCT] Coding Sequence Variant
cystatin-C precursor NP_001275543.1:p.Cys99Ser C (Cys) > S (Ser) Missense Variant
CST3 transcript variant 2 NM_001288614.2:c.296G>A C [TGT] > Y [TAT] Coding Sequence Variant
cystatin-C precursor NP_001275543.1:p.Cys99Tyr C (Cys) > Y (Tyr) Missense 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 C= A G T
GRCh38.p14 chr 20 NC_000020.11:g.23635315= NC_000020.11:g.23635315C>A NC_000020.11:g.23635315C>G NC_000020.11:g.23635315C>T
GRCh37.p13 chr 20 NC_000020.10:g.23615952= NC_000020.10:g.23615952C>A NC_000020.10:g.23615952C>G NC_000020.10:g.23615952C>T
CST3 RefSeqGene NG_012887.3:g.7623= NG_012887.3:g.7623G>T NG_012887.3:g.7623G>C NG_012887.3:g.7623G>A
CST3 transcript variant 1 NM_000099.4:c.296= NM_000099.4:c.296G>T NM_000099.4:c.296G>C NM_000099.4:c.296G>A
CST3 transcript variant 1 NM_000099.3:c.296= NM_000099.3:c.296G>T NM_000099.3:c.296G>C NM_000099.3:c.296G>A
CST3 transcript NM_000099.2:c.296= NM_000099.2:c.296G>T NM_000099.2:c.296G>C NM_000099.2:c.296G>A
CST3 transcript variant 2 NM_001288614.2:c.296= NM_001288614.2:c.296G>T NM_001288614.2:c.296G>C NM_001288614.2:c.296G>A
CST3 transcript variant 2 NM_001288614.1:c.296= NM_001288614.1:c.296G>T NM_001288614.1:c.296G>C NM_001288614.1:c.296G>A
cystatin-C precursor NP_000090.1:p.Cys99= NP_000090.1:p.Cys99Phe NP_000090.1:p.Cys99Ser NP_000090.1:p.Cys99Tyr
cystatin-C precursor NP_001275543.1:p.Cys99= NP_001275543.1:p.Cys99Phe NP_001275543.1:p.Cys99Ser NP_001275543.1:p.Cys99Tyr
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#.

5 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1693930593 Apr 01, 2015 (144)
2 GNOMAD ss2744505133 Nov 08, 2017 (151)
3 GNOMAD ss4351695581 Apr 26, 2021 (155)
4 TOPMED ss5085631288 Apr 26, 2021 (155)
5 TOPMED ss5085631289 Apr 26, 2021 (155)
6 ExAC NC_000020.10 - 23615952 Oct 12, 2018 (152)
7 gnomAD - Genomes NC_000020.11 - 23635315 Apr 26, 2021 (155)
8 gnomAD - Exomes NC_000020.10 - 23615952 Jul 13, 2019 (153)
9 TopMed

Submission ignored due to conflicting rows:
Row 360740233 (NC_000020.11:23635314:C:A 1/264690)
Row 360740234 (NC_000020.11:23635314:C:G 1/264690)

- Apr 26, 2021 (155)
10 TopMed

Submission ignored due to conflicting rows:
Row 360740233 (NC_000020.11:23635314:C:A 1/264690)
Row 360740234 (NC_000020.11:23635314:C:G 1/264690)

- Apr 26, 2021 (155)
11 ALFA NC_000020.11 - 23635315 Apr 26, 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
549222189, 11688815652, ss4351695581, ss5085631288 NC_000020.11:23635314:C:A NC_000020.11:23635314:C:A (self)
11688815652, ss5085631289 NC_000020.11:23635314:C:G NC_000020.11:23635314:C:G (self)
5480531, 13824255, ss1693930593, ss2744505133 NC_000020.10:23615951:C:T NC_000020.11:23635314: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 rs781340850

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