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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs200613531

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:112446290 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000008 (2/264690, TOPMED)
G=0.000012 (3/251374, GnomAD_exome)
G=0.000019 (3/158654, ALFA) (+ 6 more)
G=0.000016 (2/121376, ExAC)
G=0.00001 (1/78698, PAGE_STUDY)
G=0.0003 (2/6404, 1000G_30x)
G=0.0002 (1/5008, 1000G)
G=0.0003 (1/3854, ALSPAC)
G=0.0000 (0/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PTPN11 : 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 158776 A=0.999981 G=0.000019
European Sub 137962 A=0.999978 G=0.000022
African Sub 3700 A=1.0000 G=0.0000
African Others Sub 138 A=1.000 G=0.000
African American Sub 3562 A=1.0000 G=0.0000
Asian Sub 6288 A=1.0000 G=0.0000
East Asian Sub 4472 A=1.0000 G=0.0000
Other Asian Sub 1816 A=1.0000 G=0.0000
Latin American 1 Sub 442 A=1.000 G=0.000
Latin American 2 Sub 950 A=1.000 G=0.000
South Asian Sub 276 A=1.000 G=0.000
Other Sub 9158 A=1.0000 G=0.0000


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 264690 A=0.999992 G=0.000008
gnomAD - Exomes Global Study-wide 251374 A=0.999988 G=0.000012
gnomAD - Exomes European Sub 135310 A=0.999993 G=0.000007
gnomAD - Exomes Asian Sub 49010 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34588 A=0.99994 G=0.00006
gnomAD - Exomes African Sub 16254 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6134 A=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 158654 A=0.999981 G=0.000019
Allele Frequency Aggregator European Sub 137858 A=0.999978 G=0.000022
Allele Frequency Aggregator Other Sub 9154 A=1.0000 G=0.0000
Allele Frequency Aggregator Asian Sub 6288 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 3686 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 950 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 442 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 276 A=1.000 G=0.000
ExAC Global Study-wide 121376 A=0.999984 G=0.000016
ExAC Europe Sub 73348 A=0.99999 G=0.00001
ExAC Asian Sub 25166 A=1.00000 G=0.00000
ExAC American Sub 11572 A=0.99991 G=0.00009
ExAC African Sub 10382 A=1.00000 G=0.00000
ExAC Other Sub 908 A=1.000 G=0.000
The PAGE Study Global Study-wide 78698 A=0.99999 G=0.00001
The PAGE Study AfricanAmerican Sub 32516 A=1.00000 G=0.00000
The PAGE Study Mexican Sub 10808 A=1.00000 G=0.00000
The PAGE Study Asian Sub 8318 A=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7916 A=1.0000 G=0.0000
The PAGE Study NativeHawaiian Sub 4534 A=1.0000 G=0.0000
The PAGE Study Cuban Sub 4230 A=0.9998 G=0.0002
The PAGE Study Dominican Sub 3828 A=1.0000 G=0.0000
The PAGE Study CentralAmerican Sub 2450 A=1.0000 G=0.0000
The PAGE Study SouthAmerican Sub 1982 A=1.0000 G=0.0000
The PAGE Study NativeAmerican Sub 1260 A=1.0000 G=0.0000
The PAGE Study SouthAsian Sub 856 A=1.000 G=0.000
1000Genomes_30x Global Study-wide 6404 A=0.9997 G=0.0003
1000Genomes_30x African Sub 1786 A=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 A=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.998 G=0.002
1000Genomes Global Study-wide 5008 A=0.9998 G=0.0002
1000Genomes African Sub 1322 A=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.999 G=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9997 G=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=1.0000 G=0.0000
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 12 NC_000012.12:g.112446290A>G
GRCh38.p14 chr 12 NC_000012.12:g.112446290A>T
GRCh37.p13 chr 12 NC_000012.11:g.112884094A>G
GRCh37.p13 chr 12 NC_000012.11:g.112884094A>T
PTPN11 RefSeqGene (LRG_614) NG_007459.1:g.32559A>G
PTPN11 RefSeqGene (LRG_614) NG_007459.1:g.32559A>T
Gene: PTPN11, protein tyrosine phosphatase non-receptor type 11 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTPN11 transcript variant 2 NM_080601.3:c.29A>G N [AAT] > S [AGT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform 2 NP_542168.1:p.Asn10Ser N (Asn) > S (Ser) Missense Variant
PTPN11 transcript variant 2 NM_080601.3:c.29A>T N [AAT] > I [ATT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform 2 NP_542168.1:p.Asn10Ile N (Asn) > I (Ile) Missense Variant
PTPN11 transcript variant 3 NM_001330437.2:c.29A>G N [AAT] > S [AGT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform 3 NP_001317366.1:p.Asn10Ser N (Asn) > S (Ser) Missense Variant
PTPN11 transcript variant 3 NM_001330437.2:c.29A>T N [AAT] > I [ATT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform 3 NP_001317366.1:p.Asn10Ile N (Asn) > I (Ile) Missense Variant
PTPN11 transcript variant 1 NM_002834.5:c.29A>G N [AAT] > S [AGT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform 1 NP_002825.3:p.Asn10Ser N (Asn) > S (Ser) Missense Variant
PTPN11 transcript variant 1 NM_002834.5:c.29A>T N [AAT] > I [ATT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform 1 NP_002825.3:p.Asn10Ile N (Asn) > I (Ile) Missense Variant
PTPN11 transcript variant 4 NM_001374625.1:c.29A>G N [AAT] > S [AGT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform 4 NP_001361554.1:p.Asn10Ser N (Asn) > S (Ser) Missense Variant
PTPN11 transcript variant 4 NM_001374625.1:c.29A>T N [AAT] > I [ATT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform 4 NP_001361554.1:p.Asn10Ile N (Asn) > I (Ile) Missense Variant
PTPN11 transcript variant X1 XM_011538613.3:c.29A>G N [AAT] > S [AGT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform X1 XP_011536915.1:p.Asn10Ser N (Asn) > S (Ser) Missense Variant
PTPN11 transcript variant X1 XM_011538613.3:c.29A>T N [AAT] > I [ATT] Coding Sequence Variant
tyrosine-protein phosphatase non-receptor type 11 isoform X1 XP_011536915.1:p.Asn10Ile N (Asn) > I (Ile) 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 A= G T
GRCh38.p14 chr 12 NC_000012.12:g.112446290= NC_000012.12:g.112446290A>G NC_000012.12:g.112446290A>T
GRCh37.p13 chr 12 NC_000012.11:g.112884094= NC_000012.11:g.112884094A>G NC_000012.11:g.112884094A>T
PTPN11 RefSeqGene (LRG_614) NG_007459.1:g.32559= NG_007459.1:g.32559A>G NG_007459.1:g.32559A>T
PTPN11 transcript variant 1 NM_002834.5:c.29= NM_002834.5:c.29A>G NM_002834.5:c.29A>T
PTPN11 transcript variant 1 NM_002834.4:c.29= NM_002834.4:c.29A>G NM_002834.4:c.29A>T
PTPN11 transcript variant 1 NM_002834.3:c.29= NM_002834.3:c.29A>G NM_002834.3:c.29A>T
PTPN11 transcript variant 2 NM_080601.3:c.29= NM_080601.3:c.29A>G NM_080601.3:c.29A>T
PTPN11 transcript variant 2 NM_080601.2:c.29= NM_080601.2:c.29A>G NM_080601.2:c.29A>T
PTPN11 transcript variant 2 NM_080601.1:c.29= NM_080601.1:c.29A>G NM_080601.1:c.29A>T
PTPN11 transcript variant 3 NM_001330437.2:c.29= NM_001330437.2:c.29A>G NM_001330437.2:c.29A>T
PTPN11 transcript variant 3 NM_001330437.1:c.29= NM_001330437.1:c.29A>G NM_001330437.1:c.29A>T
PTPN11 transcript variant 4 NM_001374625.1:c.29= NM_001374625.1:c.29A>G NM_001374625.1:c.29A>T
PTPN11 transcript variant X1 XM_011538613.3:c.29= XM_011538613.3:c.29A>G XM_011538613.3:c.29A>T
PTPN11 transcript variant X1 XM_011538613.2:c.29= XM_011538613.2:c.29A>G XM_011538613.2:c.29A>T
PTPN11 transcript variant X2 XM_011538613.1:c.29= XM_011538613.1:c.29A>G XM_011538613.1:c.29A>T
tyrosine-protein phosphatase non-receptor type 11 isoform 1 NP_002825.3:p.Asn10= NP_002825.3:p.Asn10Ser NP_002825.3:p.Asn10Ile
tyrosine-protein phosphatase non-receptor type 11 isoform 2 NP_542168.1:p.Asn10= NP_542168.1:p.Asn10Ser NP_542168.1:p.Asn10Ile
tyrosine-protein phosphatase non-receptor type 11 isoform 3 NP_001317366.1:p.Asn10= NP_001317366.1:p.Asn10Ser NP_001317366.1:p.Asn10Ile
tyrosine-protein phosphatase non-receptor type 11 isoform 4 NP_001361554.1:p.Asn10= NP_001361554.1:p.Asn10Ser NP_001361554.1:p.Asn10Ile
tyrosine-protein phosphatase non-receptor type 11 isoform X1 XP_011536915.1:p.Asn10= XP_011536915.1:p.Asn10Ser XP_011536915.1:p.Asn10Ile
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#.

32 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss489005808 May 04, 2012 (137)
2 EXOME_CHIP ss491473936 May 04, 2012 (137)
3 ILLUMINA ss780771959 Aug 21, 2014 (142)
4 ILLUMINA ss783451645 Aug 21, 2014 (142)
5 1000GENOMES ss1346675795 Aug 21, 2014 (142)
6 EVA_UK10K_ALSPAC ss1629466334 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1672460367 Apr 01, 2015 (144)
8 EVA_EXAC ss1691118629 Apr 01, 2015 (144)
9 ILLUMINA ss1752046900 Sep 08, 2015 (146)
10 ILLUMINA ss1917879041 Feb 12, 2016 (147)
11 ILLUMINA ss1946350167 Feb 12, 2016 (147)
12 ILLUMINA ss1959466931 Feb 12, 2016 (147)
13 GNOMAD ss2740149752 Nov 08, 2017 (151)
14 ILLUMINA ss3021467226 Nov 08, 2017 (151)
15 ILLUMINA ss3626970864 Oct 12, 2018 (152)
16 ILLUMINA ss3634524199 Oct 12, 2018 (152)
17 ILLUMINA ss3640231532 Oct 12, 2018 (152)
18 ILLUMINA ss3644603169 Oct 12, 2018 (152)
19 ILLUMINA ss3651850101 Oct 12, 2018 (152)
20 ILLUMINA ss3725358270 Jul 13, 2019 (153)
21 ILLUMINA ss3744401251 Jul 13, 2019 (153)
22 ILLUMINA ss3744825013 Jul 13, 2019 (153)
23 PAGE_CC ss3771718038 Jul 13, 2019 (153)
24 ILLUMINA ss3772324215 Jul 13, 2019 (153)
25 TOPMED ss4933124174 Apr 26, 2021 (155)
26 1000G_HIGH_COVERAGE ss5292266395 Oct 16, 2022 (156)
27 EVA ss5408288241 Oct 16, 2022 (156)
28 1000G_HIGH_COVERAGE ss5590509419 Oct 16, 2022 (156)
29 EVA ss5847683997 Oct 16, 2022 (156)
30 EVA ss5906059472 Oct 16, 2022 (156)
31 EVA ss5936146550 Oct 16, 2022 (156)
32 EVA ss5945381855 Oct 16, 2022 (156)
33 1000Genomes NC_000012.11 - 112884094 Oct 12, 2018 (152)
34 1000Genomes_30x NC_000012.12 - 112446290 Oct 16, 2022 (156)
35 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 112884094 Oct 12, 2018 (152)
36 ExAC NC_000012.11 - 112884094 Oct 12, 2018 (152)
37 gnomAD - Exomes NC_000012.11 - 112884094 Jul 13, 2019 (153)
38 The PAGE Study NC_000012.12 - 112446290 Jul 13, 2019 (153)
39 TopMed NC_000012.12 - 112446290 Apr 26, 2021 (155)
40 UK 10K study - Twins NC_000012.11 - 112884094 Oct 12, 2018 (152)
41 ALFA NC_000012.12 - 112446290 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
59487951, 33039125, 1433754, 9388075, 33039125, ss489005808, ss491473936, ss780771959, ss783451645, ss1346675795, ss1629466334, ss1672460367, ss1691118629, ss1752046900, ss1917879041, ss1946350167, ss1959466931, ss2740149752, ss3021467226, ss3626970864, ss3634524199, ss3640231532, ss3644603169, ss3651850101, ss3744401251, ss3744825013, ss3772324215, ss5408288241, ss5847683997, ss5945381855 NC_000012.11:112884093:A:G NC_000012.12:112446289:A:G (self)
78035354, 939507, 148669831, 5359344768, ss3725358270, ss3771718038, ss4933124174, ss5292266395, ss5590509419, ss5906059472 NC_000012.12:112446289:A:G NC_000012.12:112446289:A:G (self)
ss5936146550 NC_000012.11:112884093:A:T NC_000012.12:112446289:A:T
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 rs200613531

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