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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.

rs139217250

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:54263826 (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=0.000004 (1/251276, GnomAD_exome)
G=0.000014 (2/140228, GnomAD) (+ 2 more)
G=0.00000 (0/14050, ALFA)
G=0.00008 (1/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PDGFRA : 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 A=1.00000 G=0.00000
European Sub 9690 A=1.0000 G=0.0000
African Sub 2898 A=1.0000 G=0.0000
African Others Sub 114 A=1.000 G=0.000
African American Sub 2784 A=1.0000 G=0.0000
Asian Sub 112 A=1.000 G=0.000
East Asian Sub 86 A=1.00 G=0.00
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 146 A=1.000 G=0.000
Latin American 2 Sub 610 A=1.000 G=0.000
South Asian Sub 98 A=1.00 G=0.00
Other Sub 496 A=1.000 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
TopMed Global Study-wide 264690 A=0.999992 G=0.000008
gnomAD - Exomes Global Study-wide 251276 A=0.999996 G=0.000004
gnomAD - Exomes European Sub 135278 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 49004 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34538 A=1.00000 G=0.00000
gnomAD - Exomes African Sub 16254 A=0.99994 G=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10074 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6128 A=1.0000 G=0.0000
gnomAD - Genomes Global Study-wide 140228 A=0.999986 G=0.000014
gnomAD - Genomes European Sub 75934 A=1.00000 G=0.00000
gnomAD - Genomes African Sub 42034 A=0.99995 G=0.00005
gnomAD - Genomes American Sub 13656 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 A=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 14050 A=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13006 A=0.99992 G=0.00008
GO Exome Sequencing Project European American Sub 8600 A=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 4406 A=0.9998 G=0.0002
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 4 NC_000004.12:g.54263826A>G
GRCh38.p14 chr 4 NC_000004.12:g.54263826A>T
GRCh37.p13 chr 4 NC_000004.11:g.55129993A>G
GRCh37.p13 chr 4 NC_000004.11:g.55129993A>T
PDGFRA RefSeqGene (LRG_309) NG_009250.1:g.39730A>G
PDGFRA RefSeqGene (LRG_309) NG_009250.1:g.39730A>T
Gene: PDGFRA, platelet derived growth factor receptor alpha (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PDGFRA transcript variant 1 NM_006206.6:c.527A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 1 precursor NP_006197.1:p.Gln176Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant 1 NM_006206.6:c.527A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 1 precursor NP_006197.1:p.Gln176Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant 2 NM_001347827.2:c.527A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 2 precursor NP_001334756.1:p.Gln176Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant 2 NM_001347827.2:c.527A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 2 precursor NP_001334756.1:p.Gln176Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant 5 NM_001347829.2:c.527A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 1 precursor NP_001334758.1:p.Gln176Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant 5 NM_001347829.2:c.527A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 1 precursor NP_001334758.1:p.Gln176Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant 3 NM_001347828.2:c.602A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 3 NP_001334757.1:p.Gln201Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant 3 NM_001347828.2:c.602A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 3 NP_001334757.1:p.Gln201Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant 4 NM_001347830.2:c.566A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 4 NP_001334759.1:p.Gln189Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant 4 NM_001347830.2:c.566A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform 4 NP_001334759.1:p.Gln189Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant X1 XM_005265743.2:c.527A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X1 XP_005265800.1:p.Gln176Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant X1 XM_005265743.2:c.527A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X1 XP_005265800.1:p.Gln176Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant X2 XM_047415766.1:c.527A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X1 XP_047271722.1:p.Gln176Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant X2 XM_047415766.1:c.527A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X1 XP_047271722.1:p.Gln176Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant X3 XM_047415767.1:c.527A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X1 XP_047271723.1:p.Gln176Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant X3 XM_047415767.1:c.527A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X1 XP_047271723.1:p.Gln176Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant X4 XM_006714041.4:c.602A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X2 XP_006714104.1:p.Gln201Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant X4 XM_006714041.4:c.602A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X2 XP_006714104.1:p.Gln201Leu Q (Gln) > L (Leu) Missense Variant
PDGFRA transcript variant X5 XM_017008281.2:c.566A>G Q [CAG] > R [CGG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X3 XP_016863770.1:p.Gln189Arg Q (Gln) > R (Arg) Missense Variant
PDGFRA transcript variant X5 XM_017008281.2:c.566A>T Q [CAG] > L [CTG] Coding Sequence Variant
platelet-derived growth factor receptor alpha isoform X3 XP_016863770.1:p.Gln189Leu Q (Gln) > L (Leu) 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.

Allele: G (allele ID: 520288 )
ClinVar Accession Disease Names Clinical Significance
RCV000633840.5 Gastrointestinal stromal tumor Uncertain-Significance
RCV001023851.1 Hereditary cancer-predisposing syndrome Uncertain-Significance
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 4 NC_000004.12:g.54263826= NC_000004.12:g.54263826A>G NC_000004.12:g.54263826A>T
GRCh37.p13 chr 4 NC_000004.11:g.55129993= NC_000004.11:g.55129993A>G NC_000004.11:g.55129993A>T
PDGFRA RefSeqGene (LRG_309) NG_009250.1:g.39730= NG_009250.1:g.39730A>G NG_009250.1:g.39730A>T
PDGFRA transcript variant 1 NM_006206.6:c.527= NM_006206.6:c.527A>G NM_006206.6:c.527A>T
PDGFRA transcript variant 1 NM_006206.5:c.527= NM_006206.5:c.527A>G NM_006206.5:c.527A>T
PDGFRA transcript NM_006206.4:c.527= NM_006206.4:c.527A>G NM_006206.4:c.527A>T
PDGFRA transcript variant 4 NM_001347830.2:c.566= NM_001347830.2:c.566A>G NM_001347830.2:c.566A>T
PDGFRA transcript variant 4 NM_001347830.1:c.566= NM_001347830.1:c.566A>G NM_001347830.1:c.566A>T
PDGFRA transcript variant 5 NM_001347829.2:c.527= NM_001347829.2:c.527A>G NM_001347829.2:c.527A>T
PDGFRA transcript variant 5 NM_001347829.1:c.527= NM_001347829.1:c.527A>G NM_001347829.1:c.527A>T
PDGFRA transcript variant 3 NM_001347828.2:c.602= NM_001347828.2:c.602A>G NM_001347828.2:c.602A>T
PDGFRA transcript variant 3 NM_001347828.1:c.602= NM_001347828.1:c.602A>G NM_001347828.1:c.602A>T
PDGFRA transcript variant 2 NM_001347827.2:c.527= NM_001347827.2:c.527A>G NM_001347827.2:c.527A>T
PDGFRA transcript variant 2 NM_001347827.1:c.527= NM_001347827.1:c.527A>G NM_001347827.1:c.527A>T
PDGFRA transcript variant X4 XM_006714041.4:c.602= XM_006714041.4:c.602A>G XM_006714041.4:c.602A>T
PDGFRA transcript variant X2 XM_006714041.3:c.602= XM_006714041.3:c.602A>G XM_006714041.3:c.602A>T
PDGFRA transcript variant X5 XM_006714041.2:c.602= XM_006714041.2:c.602A>G XM_006714041.2:c.602A>T
PDGFRA transcript variant X4 XM_006714041.1:c.602= XM_006714041.1:c.602A>G XM_006714041.1:c.602A>T
PDGFRA transcript variant X1 XM_005265743.2:c.527= XM_005265743.2:c.527A>G XM_005265743.2:c.527A>T
PDGFRA transcript variant X1 XM_005265743.1:c.527= XM_005265743.1:c.527A>G XM_005265743.1:c.527A>T
PDGFRA transcript variant X5 XM_017008281.2:c.566= XM_017008281.2:c.566A>G XM_017008281.2:c.566A>T
PDGFRA transcript variant X3 XM_017008281.1:c.566= XM_017008281.1:c.566A>G XM_017008281.1:c.566A>T
PDGFRA transcript variant X3 XM_047415767.1:c.527= XM_047415767.1:c.527A>G XM_047415767.1:c.527A>T
PDGFRA transcript variant X2 XM_047415766.1:c.527= XM_047415766.1:c.527A>G XM_047415766.1:c.527A>T
platelet-derived growth factor receptor alpha isoform 1 precursor NP_006197.1:p.Gln176= NP_006197.1:p.Gln176Arg NP_006197.1:p.Gln176Leu
platelet-derived growth factor receptor alpha isoform 4 NP_001334759.1:p.Gln189= NP_001334759.1:p.Gln189Arg NP_001334759.1:p.Gln189Leu
platelet-derived growth factor receptor alpha isoform 1 precursor NP_001334758.1:p.Gln176= NP_001334758.1:p.Gln176Arg NP_001334758.1:p.Gln176Leu
platelet-derived growth factor receptor alpha isoform 3 NP_001334757.1:p.Gln201= NP_001334757.1:p.Gln201Arg NP_001334757.1:p.Gln201Leu
platelet-derived growth factor receptor alpha isoform 2 precursor NP_001334756.1:p.Gln176= NP_001334756.1:p.Gln176Arg NP_001334756.1:p.Gln176Leu
platelet-derived growth factor receptor alpha isoform X2 XP_006714104.1:p.Gln201= XP_006714104.1:p.Gln201Arg XP_006714104.1:p.Gln201Leu
platelet-derived growth factor receptor alpha isoform X1 XP_005265800.1:p.Gln176= XP_005265800.1:p.Gln176Arg XP_005265800.1:p.Gln176Leu
platelet-derived growth factor receptor alpha isoform X3 XP_016863770.1:p.Gln189= XP_016863770.1:p.Gln189Arg XP_016863770.1:p.Gln189Leu
platelet-derived growth factor receptor alpha isoform X1 XP_047271723.1:p.Gln176= XP_047271723.1:p.Gln176Arg XP_047271723.1:p.Gln176Leu
platelet-derived growth factor receptor alpha isoform X1 XP_047271722.1:p.Gln176= XP_047271722.1:p.Gln176Arg XP_047271722.1:p.Gln176Leu
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#.

7 SubSNP, 5 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342163411 May 09, 2011 (134)
2 GNOMAD ss2734510638 Nov 08, 2017 (151)
3 GNOMAD ss2747238378 Nov 08, 2017 (151)
4 GNOMAD ss2809117530 Nov 08, 2017 (151)
5 EVA ss3824016059 Apr 26, 2020 (154)
6 TOPMED ss4613296258 Apr 26, 2021 (155)
7 EVA ss5935698270 Oct 13, 2022 (156)
8 gnomAD - Genomes NC_000004.12 - 54263826 Apr 26, 2021 (155)
9 gnomAD - Exomes NC_000004.11 - 55129993 Jul 13, 2019 (153)
10 GO Exome Sequencing Project NC_000004.11 - 55129993 Oct 12, 2018 (152)
11 TopMed NC_000004.12 - 54263826 Apr 26, 2021 (155)
12 ALFA NC_000004.12 - 54263826 Apr 26, 2021 (155)
13 ClinVar RCV000633840.5 Oct 13, 2022 (156)
14 ClinVar RCV001023851.1 Apr 26, 2020 (154)
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
3613603, 474284, ss342163411, ss2734510638, ss2747238378, ss2809117530, ss3824016059 NC_000004.11:55129992:A:G NC_000004.12:54263825:A:G (self)
RCV000633840.5, RCV001023851.1, 149284478, 450673814, 4953060260, ss4613296258 NC_000004.12:54263825:A:G NC_000004.12:54263825:A:G (self)
ss5935698270 NC_000004.11:55129992:A:T NC_000004.12:54263825: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 rs139217250

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