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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.

rs376978985

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:150115787 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000083 (22/264690, TOPMED)
T=0.000069 (17/246610, GnomAD_exome)
T=0.000021 (3/140292, GnomAD) (+ 3 more)
T=0.000088 (10/113280, ExAC)
T=0.00011 (4/35290, ALFA)
T=0.00008 (1/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PDGFRB : Synonymous 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 35290 C=0.99989 T=0.00011
European Sub 26478 C=0.99996 T=0.00004
African Sub 2918 C=0.9997 T=0.0003
African Others Sub 114 C=1.000 T=0.000
African American Sub 2804 C=0.9996 T=0.0004
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 494 C=1.000 T=0.000
Latin American 2 Sub 628 C=1.000 T=0.000
South Asian Sub 98 C=0.99 T=0.01
Other Sub 4562 C=0.9998 T=0.0002


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 C=0.999917 T=0.000083
gnomAD - Exomes Global Study-wide 246610 C=0.999931 T=0.000069
gnomAD - Exomes European Sub 132542 C=0.999970 T=0.000030
gnomAD - Exomes Asian Sub 48406 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 33916 C=0.99971 T=0.00029
gnomAD - Exomes African Sub 15882 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 9880 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5984 C=0.9997 T=0.0003
gnomAD - Genomes Global Study-wide 140292 C=0.999979 T=0.000021
gnomAD - Genomes European Sub 75964 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 42050 C=0.99998 T=0.00002
gnomAD - Genomes American Sub 13666 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 113280 C=0.999912 T=0.000088
ExAC Europe Sub 68972 C=0.99999 T=0.00001
ExAC Asian Sub 22994 C=1.00000 T=0.00000
ExAC American Sub 11294 C=0.99938 T=0.00062
ExAC African Sub 9206 C=0.9998 T=0.0002
ExAC Other Sub 814 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 35290 C=0.99989 T=0.00011
Allele Frequency Aggregator European Sub 26478 C=0.99996 T=0.00004
Allele Frequency Aggregator Other Sub 4562 C=0.9998 T=0.0002
Allele Frequency Aggregator African Sub 2918 C=0.9997 T=0.0003
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 494 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=0.99 T=0.01
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9998 T=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 5 NC_000005.10:g.150115787C>T
GRCh37.p13 chr 5 NC_000005.9:g.149495350C>T
CSF1R RefSeqGene NG_012303.2:g.2586G>A
PDGFRB RefSeqGene NG_023367.1:g.45073G>A
Gene: PDGFRB, platelet derived growth factor receptor beta (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PDGFRB transcript variant 1 NM_002609.4:c.3297G>A A [GCG] > A [GCA] Coding Sequence Variant
platelet-derived growth factor receptor beta isoform 1 precursor NP_002600.1:p.Ala1099= A (Ala) > A (Ala) Synonymous Variant
PDGFRB transcript variant 2 NM_001355016.2:c.3105G>A A [GCG] > A [GCA] Coding Sequence Variant
platelet-derived growth factor receptor beta isoform 2 NP_001341945.1:p.Ala1035= A (Ala) > A (Ala) Synonymous Variant
PDGFRB transcript variant 3 NM_001355017.2:c.2814G>A A [GCG] > A [GCA] Coding Sequence Variant
platelet-derived growth factor receptor beta isoform 3 NP_001341946.1:p.Ala938= A (Ala) > A (Ala) Synonymous 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: T (allele ID: 749342 )
ClinVar Accession Disease Names Clinical Significance
RCV000924831.3 not provided Likely-Benign
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= T
GRCh38.p14 chr 5 NC_000005.10:g.150115787= NC_000005.10:g.150115787C>T
GRCh37.p13 chr 5 NC_000005.9:g.149495350= NC_000005.9:g.149495350C>T
CSF1R RefSeqGene NG_012303.2:g.2586= NG_012303.2:g.2586G>A
PDGFRB RefSeqGene NG_023367.1:g.45073= NG_023367.1:g.45073G>A
PDGFRB transcript variant 1 NM_002609.4:c.3297= NM_002609.4:c.3297G>A
PDGFRB transcript variant 1 NM_002609.3:c.3297= NM_002609.3:c.3297G>A
PDGFRB transcript variant 3 NM_001355017.2:c.2814= NM_001355017.2:c.2814G>A
PDGFRB transcript variant 3 NM_001355017.1:c.2814= NM_001355017.1:c.2814G>A
PDGFRB transcript variant 2 NM_001355016.2:c.3105= NM_001355016.2:c.3105G>A
PDGFRB transcript variant 2 NM_001355016.1:c.3105= NM_001355016.1:c.3105G>A
platelet-derived growth factor receptor beta isoform 1 precursor NP_002600.1:p.Ala1099= NP_002600.1:p.Ala1099=
platelet-derived growth factor receptor beta isoform 3 NP_001341946.1:p.Ala938= NP_001341946.1:p.Ala938=
platelet-derived growth factor receptor beta isoform 2 NP_001341945.1:p.Ala1035= NP_001341945.1:p.Ala1035=
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#.

9 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712669810 Apr 25, 2013 (138)
2 EVA_EXAC ss1688037689 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2279232192 Dec 20, 2016 (150)
4 GNOMAD ss2735353101 Nov 08, 2017 (151)
5 GNOMAD ss2747488743 Nov 08, 2017 (151)
6 GNOMAD ss2832248785 Nov 08, 2017 (151)
7 EVA ss3824129583 Apr 26, 2020 (154)
8 TOPMED ss4683209629 Apr 26, 2021 (155)
9 EVA ss5935777597 Oct 13, 2022 (156)
10 ExAC NC_000005.9 - 149495350 Oct 12, 2018 (152)
11 gnomAD - Genomes NC_000005.10 - 150115787 Apr 26, 2021 (155)
12 gnomAD - Exomes NC_000005.9 - 149495350 Jul 13, 2019 (153)
13 GO Exome Sequencing Project NC_000005.9 - 149495350 Oct 12, 2018 (152)
14 TopMed NC_000005.10 - 150115787 Apr 26, 2021 (155)
15 ALFA NC_000005.10 - 150115787 Apr 26, 2021 (155)
16 ClinVar RCV000924831.3 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
8047317, 4484723, 587664, ss712669810, ss1688037689, ss2735353101, ss2747488743, ss2832248785, ss3824129583, ss5935777597 NC_000005.9:149495349:C:T NC_000005.10:150115786:C:T (self)
RCV000924831.3, 208144051, 520587186, 8423794513, ss2279232192, ss4683209629 NC_000005.10:150115786:C:T NC_000005.10:150115786: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 rs376978985

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