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dbSNP Short Genetic Variations

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.

rs10959

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr22:24653231 (GRCh38.p12) 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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00002 (3/125568, TOPMED)
T=0.0005 (15/30124, GnomAD)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BCRP3 : Non Coding Transcript Variant
POM121L10P : Non Coding Transcript Variant
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.p12 chr 22 NC_000022.11:g.24653231G>A
GRCh38.p12 chr 22 NC_000022.11:g.24653231G>T
GRCh37.p13 chr 22 NC_000022.10:g.25049198G>A
GRCh37.p13 chr 22 NC_000022.10:g.25049198G>T
Gene: BCRP3, breakpoint cluster region pseudogene 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BCRP3 transcript NR_024494.1:n.1296G>A N/A Non Coding Transcript Variant
BCRP3 transcript NR_024494.1:n.1296G>T N/A Non Coding Transcript Variant
Gene: POM121L10P, POM121 transmembrane nucleoporin like 10, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
POM121L10P transcript NR_024593.1:n.5917C>T N/A Non Coding Transcript Variant
POM121L10P transcript NR_024593.1:n.5917C>A N/A Non Coding 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

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
TopMed Global Study-wide 125568 G=0.99998 A=0.00002
gnomAD - Genomes Global Study-wide 30124 G=0.9995 T=0.0005, A=0.0000
gnomAD - Genomes European Sub 17850 G=0.9992 T=0.0007, A=0.0001
gnomAD - Genomes African Sub 8654 G=1.000 T=0.000, A=0.000
gnomAD - Genomes East Asian Sub 1594 G=0.999 T=0.001, A=0.000
gnomAD - Genomes Other Sub 934 G=1.00 T=0.00, A=0.00
gnomAD - Genomes American Sub 824 G=1.00 T=0.00, A=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 268 G=1.00 T=0.00, A=0.00
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 T Note
GRCh38.p12 chr 22 NC_000022.11:g.24...

NC_000022.11:g.24653231G=

NC_000022.11:g.24...

NC_000022.11:g.24653231G>A

NC_000022.11:g.24...

NC_000022.11:g.24653231G>T

GRCh37.p13 chr 22 NC_000022.10:g.25...

NC_000022.10:g.25049198G=

NC_000022.10:g.25...

NC_000022.10:g.25049198G>A

NC_000022.10:g.25...

NC_000022.10:g.25049198G>T

POM121L10P transcript NR_024593.1:n.5917C= NR_024593.1:n.591...

NR_024593.1:n.5917C>T

NR_024593.1:n.591...

NR_024593.1:n.5917C>A

BCRP3 transcript NR_024494.1:n.1296G= NR_024494.1:n.129...

NR_024494.1:n.1296G>A

NR_024494.1:n.129...

NR_024494.1:n.1296G>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#.

8 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss13137 Sep 19, 2000 (52)
2 SC_JCM ss11340303 Jul 11, 2003 (144)
3 SC_SNP ss13388965 Dec 05, 2003 (121)
4 SSAHASNP ss35491769 May 24, 2005 (142)
5 TOPMED ss2413569978 Dec 20, 2016 (150)
6 GNOMAD ss2973430275 Nov 08, 2017 (151)
7 TOPMED ss3374983725 Nov 08, 2017 (151)
8 TOPMED ss3374983726 Nov 08, 2017 (151)
9 gnomAD - Genomes NC_000022.10 - 25049198 Oct 12, 2018 (152)
10 TopMed NC_000022.11 - 24653231 Oct 12, 2018 (152)
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).

Associated ID History Updated (Build)
rs3183300 Jul 03, 2002 (106)
rs3896501 Feb 27, 2004 (120)
rs3984057 Apr 21, 2003 (114)
rs4050042 Jul 01, 2015 (144)
rs4050420 Feb 27, 2004 (120)
rs4050666 Sep 24, 2004 (123)
rs4051356 Dec 16, 2002 (110)
rs4052047 Dec 16, 2002 (110)
rs4052287 Sep 24, 2004 (123)
rs7511565 Sep 24, 2004 (123)
rs9605810 Feb 27, 2004 (120)
rs9624532 Apr 05, 2004 (121)
rs17000441 Mar 10, 2006 (126)
rs28688846 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
126784141, ss2413569978, ss2973430275 NC_000022.10:25049197:G:A NC_000022.11:24653230:G:A (self)
238174588, ss3374983725 NC_000022.11:24653230:G:A NC_000022.11:24653230:G:A (self)
ss35491769 NC_000022.8:23373751:G:T NC_000022.11:24653230:G:T (self)
126784141, ss2973430275 NC_000022.10:25049197:G:T NC_000022.11:24653230:G:T (self)
ss3374983726 NC_000022.11:24653230:G:T NC_000022.11:24653230:G:T (self)
ss11340303, ss13388965 NT_011520.9:4439766:G:T NC_000022.11:24653230:G:T (self)
ss13137 NT_011520.12:4439766:G:T NC_000022.11:24653230:G: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 rs10959

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.post104+4a6ee9c