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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.

rs138830253

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:150134962 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000023 (6/264690, TOPMED)
A=0.000036 (9/251038, GnomAD_exome)
A=0.000058 (10/172746, ALFA) (+ 4 more)
A=0.000014 (2/140256, GnomAD)
A=0.000083 (10/120424, ExAC)
A=0.00001 (1/78702, PAGE_STUDY)
A=0.00008 (1/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PDGFRB : 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 189158 G=0.999942 A=0.000058
European Sub 163048 G=0.999939 A=0.000061
African Sub 9724 G=1.0000 A=0.0000
African Others Sub 360 G=1.000 A=0.000
African American Sub 9364 G=1.0000 A=0.0000
Asian Sub 3394 G=1.0000 A=0.0000
East Asian Sub 2712 G=1.0000 A=0.0000
Other Asian Sub 682 G=1.000 A=0.000
Latin American 1 Sub 442 G=1.000 A=0.000
Latin American 2 Sub 950 G=1.000 A=0.000
South Asian Sub 280 G=1.000 A=0.000
Other Sub 11320 G=0.99991 A=0.00009


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 G=0.999977 A=0.000023
gnomAD - Exomes Global Study-wide 251038 G=0.999964 A=0.000036
gnomAD - Exomes European Sub 135132 G=0.999948 A=0.000052
gnomAD - Exomes Asian Sub 48936 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34528 G=0.99994 A=0.00006
gnomAD - Exomes African Sub 16248 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10068 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6126 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 172746 G=0.999942 A=0.000058
Allele Frequency Aggregator European Sub 152908 G=0.999941 A=0.000059
Allele Frequency Aggregator Other Sub 9886 G=0.9999 A=0.0001
Allele Frequency Aggregator African Sub 4886 G=1.0000 A=0.0000
Allele Frequency Aggregator Asian Sub 3394 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 950 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 442 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 280 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 140256 G=0.999986 A=0.000014
gnomAD - Genomes European Sub 75962 G=0.99997 A=0.00003
gnomAD - Genomes African Sub 42032 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13654 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
ExAC Global Study-wide 120424 G=0.999917 A=0.000083
ExAC Europe Sub 73140 G=0.99989 A=0.00011
ExAC Asian Sub 24412 G=0.99996 A=0.00004
ExAC American Sub 11572 G=0.99991 A=0.00009
ExAC African Sub 10400 G=1.00000 A=0.00000
ExAC Other Sub 900 G=1.000 A=0.000
The PAGE Study Global Study-wide 78702 G=0.99999 A=0.00001
The PAGE Study AfricanAmerican Sub 32516 G=1.00000 A=0.00000
The PAGE Study Mexican Sub 10810 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8600 G=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 4406 G=1.0000 A=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 5 NC_000005.10:g.150134962G>A
GRCh37.p13 chr 5 NC_000005.9:g.149514525G>A
PDGFRB RefSeqGene NG_023367.1:g.25898C>T
Gene: PDGFRB, platelet derived growth factor receptor beta (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PDGFRB transcript variant 3 NM_001355017.2:c.-99= N/A 5 Prime UTR Variant
PDGFRB transcript variant 1 NM_002609.4:c.419C>T T [ACG] > M [ATG] Coding Sequence Variant
platelet-derived growth factor receptor beta isoform 1 precursor NP_002600.1:p.Thr140Met T (Thr) > M (Met) Missense Variant
PDGFRB transcript variant 2 NM_001355016.2:c.227C>T T [ACG] > M [ATG] Coding Sequence Variant
platelet-derived growth factor receptor beta isoform 2 NP_001341945.1:p.Thr76Met T (Thr) > M (Met) Missense Variant
PDGFRB transcript variant 4 NR_149150.2:n. N/A Genic Downstream 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.

Allele: A (allele ID: 1295080 )
ClinVar Accession Disease Names Clinical Significance
RCV001765041.1 not provided 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 G= A
GRCh38.p14 chr 5 NC_000005.10:g.150134962= NC_000005.10:g.150134962G>A
GRCh37.p13 chr 5 NC_000005.9:g.149514525= NC_000005.9:g.149514525G>A
PDGFRB RefSeqGene NG_023367.1:g.25898= NG_023367.1:g.25898C>T
PDGFRB transcript variant 1 NM_002609.4:c.419= NM_002609.4:c.419C>T
PDGFRB transcript variant 1 NM_002609.3:c.419= NM_002609.3:c.419C>T
PDGFRB transcript variant 3 NM_001355017.2:c.-99= NM_001355017.2:c.-99C>T
PDGFRB transcript variant 3 NM_001355017.1:c.-99= NM_001355017.1:c.-99C>T
PDGFRB transcript variant 2 NM_001355016.2:c.227= NM_001355016.2:c.227C>T
PDGFRB transcript variant 2 NM_001355016.1:c.227= NM_001355016.1:c.227C>T
platelet-derived growth factor receptor beta isoform 1 precursor NP_002600.1:p.Thr140= NP_002600.1:p.Thr140Met
platelet-derived growth factor receptor beta isoform 2 NP_001341945.1:p.Thr76= NP_001341945.1:p.Thr76Met
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, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342194102 May 09, 2011 (134)
2 EXOME_CHIP ss491373997 May 04, 2012 (137)
3 ILLUMINA ss780842701 Sep 08, 2015 (146)
4 ILLUMINA ss783526084 Sep 08, 2015 (146)
5 EVA_EXAC ss1688038620 Apr 01, 2015 (144)
6 ILLUMINA ss1752556054 Sep 08, 2015 (146)
7 ILLUMINA ss1917796098 Feb 12, 2016 (147)
8 ILLUMINA ss1946159386 Feb 12, 2016 (147)
9 ILLUMINA ss1958834086 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2279233458 Dec 20, 2016 (150)
11 GNOMAD ss2735354372 Nov 08, 2017 (151)
12 AFFY ss2985339734 Nov 08, 2017 (151)
13 SWEGEN ss2997997240 Nov 08, 2017 (151)
14 ILLUMINA ss3022542305 Nov 08, 2017 (151)
15 ILLUMINA ss3629370529 Oct 12, 2018 (152)
16 ILLUMINA ss3635028734 Oct 12, 2018 (152)
17 ILLUMINA ss3640736028 Oct 12, 2018 (152)
18 ILLUMINA ss3644892392 Oct 12, 2018 (152)
19 ILLUMINA ss3653045416 Oct 12, 2018 (152)
20 ILLUMINA ss3654111933 Oct 12, 2018 (152)
21 ILLUMINA ss3726281927 Jul 13, 2019 (153)
22 ILLUMINA ss3744542302 Jul 13, 2019 (153)
23 ILLUMINA ss3745328907 Jul 13, 2019 (153)
24 PAGE_CC ss3771240059 Jul 13, 2019 (153)
25 ILLUMINA ss3772822847 Jul 13, 2019 (153)
26 EVA ss3824129793 Apr 26, 2020 (154)
27 GNOMAD ss4131622677 Apr 26, 2021 (155)
28 TOPMED ss4683214453 Apr 26, 2021 (155)
29 EVA ss5361788867 Oct 13, 2022 (156)
30 EVA ss5848069657 Oct 13, 2022 (156)
31 EVA ss5935779233 Oct 13, 2022 (156)
32 EVA ss5967615387 Oct 13, 2022 (156)
33 ExAC NC_000005.9 - 149514525 Oct 12, 2018 (152)
34 gnomAD - Genomes NC_000005.10 - 150134962 Apr 26, 2021 (155)
35 gnomAD - Exomes NC_000005.9 - 149514525 Jul 13, 2019 (153)
36 GO Exome Sequencing Project NC_000005.9 - 149514525 Oct 12, 2018 (152)
37 The PAGE Study NC_000005.10 - 150134962 Jul 13, 2019 (153)
38 TopMed NC_000005.10 - 150134962 Apr 26, 2021 (155)
39 ALFA NC_000005.10 - 150134962 Apr 26, 2021 (155)
40 ClinVar RCV001765041.1 Oct 13, 2022 (156)
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
8048279, 4486049, 587874, ss342194102, ss491373997, ss780842701, ss783526084, ss1688038620, ss1752556054, ss1917796098, ss1946159386, ss1958834086, ss2735354372, ss2985339734, ss2997997240, ss3022542305, ss3629370529, ss3635028734, ss3640736028, ss3644892392, ss3653045416, ss3654111933, ss3744542302, ss3745328907, ss3772822847, ss3824129793, ss5361788867, ss5848069657, ss5935779233, ss5967615387 NC_000005.9:149514524:G:A NC_000005.10:150134961:G:A (self)
RCV001765041.1, 208148084, 461528, 520592010, 5424973478, ss2279233458, ss3726281927, ss3771240059, ss4131622677, ss4683214453 NC_000005.10:150134961:G:A NC_000005.10:150134961:G:A (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 rs138830253

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