Name: rs202160957
Published: September 21, 2022
License: Open Access

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.

rs202160957

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:150115725 (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 / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.00297 (84/28258, 14KJPN)
A=0.00004 (1/27488, ALFA)
T=0.00004 (1/27488, ALFA) (+ 8 more)
C=0.00352 (59/16760, 8.3KJPN)
C=0.0002 (1/6404, 1000G_30x)
C=0.0002 (1/5008, 1000G)
T=0.0002 (1/4480, Estonian)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
C=0.0068 (20/2922, KOREAN)
C=0.0076 (14/1832, Korea1K)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PDGFRB : 3 Prime UTR 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	27488	G=0.99993	A=0.00004, C=0.00000, T=0.00004
European	Sub	20204	G=0.99995	A=0.00000, C=0.00000, T=0.00005
African	Sub	3488	G=1.0000	A=0.0000, C=0.0000, T=0.0000
African Others	Sub	122	G=1.000	A=0.000, C=0.000, T=0.000
African American	Sub	3366	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Asian	Sub	168	G=1.000	A=0.000, C=0.000, T=0.000
East Asian	Sub	112	G=1.000	A=0.000, C=0.000, T=0.000
Other Asian	Sub	56	G=1.00	A=0.00, C=0.00, T=0.00
Latin American 1	Sub	146	G=1.000	A=0.000, C=0.000, T=0.000
Latin American 2	Sub	610	G=1.000	A=0.000, C=0.000, T=0.000
South Asian	Sub	98	G=1.00	A=0.00, C=0.00, T=0.00
Other	Sub	2774	G=0.9996	A=0.0004, C=0.0000, T=0.0000

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
14KJPN	JAPANESE	Study-wide	28258	G=0.99703	C=0.00297
Allele Frequency Aggregator	Total	Global	27488	G=0.99993	A=0.00004, C=0.00000, T=0.00004
Allele Frequency Aggregator	European	Sub	20204	G=0.99995	A=0.00000, C=0.00000, T=0.00005
Allele Frequency Aggregator	African	Sub	3488	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	2774	G=0.9996	A=0.0004, C=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	168	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00, C=0.00, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99648	C=0.00352
1000Genomes_30x	Global	Study-wide	6404	G=0.9998	C=0.0002
1000Genomes_30x	African	Sub	1786	G=1.0000	C=0.0000
1000Genomes_30x	Europe	Sub	1266	G=1.0000	C=0.0000
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	C=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=0.9991	C=0.0009
1000Genomes_30x	American	Sub	980	G=1.000	C=0.000
1000Genomes	Global	Study-wide	5008	G=0.9998	C=0.0002
1000Genomes	African	Sub	1322	G=1.0000	C=0.0000
1000Genomes	East Asian	Sub	1008	G=0.9990	C=0.0010
1000Genomes	Europe	Sub	1006	G=1.0000	C=0.0000
1000Genomes	South Asian	Sub	978	G=1.000	C=0.000
1000Genomes	American	Sub	694	G=1.000	C=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9998	T=0.0002
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9997	T=0.0003
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=1.0000	T=0.0000
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9932	A=0.0000, C=0.0068
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9924	C=0.0076

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.150115725G>A
GRCh38.p14 chr 5	NC_000005.10:g.150115725G>C
GRCh38.p14 chr 5	NC_000005.10:g.150115725G>T
GRCh37.p13 chr 5	NC_000005.9:g.149495288G>A
GRCh37.p13 chr 5	NC_000005.9:g.149495288G>C
GRCh37.p13 chr 5	NC_000005.9:g.149495288G>T
CSF1R RefSeqGene	NG_012303.2:g.2648C>T
CSF1R RefSeqGene	NG_012303.2:g.2648C>G
CSF1R RefSeqGene	NG_012303.2:g.2648C>A
PDGFRB RefSeqGene	NG_023367.1:g.45135C>T
PDGFRB RefSeqGene	NG_023367.1:g.45135C>G
PDGFRB RefSeqGene	NG_023367.1:g.45135C>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.*38=	N/A	3 Prime UTR Variant
PDGFRB transcript variant 2	NM_001355016.2:c.*38=	N/A	3 Prime UTR Variant
PDGFRB transcript variant 3	NM_001355017.2:c.*38=	N/A	3 Prime UTR Variant
PDGFRB transcript variant 4	NR_149150.2:n.	N/A	Genic Downstream Transcript Variant

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

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	C	T
GRCh38.p14 chr 5	NC_000005.10:g.150115725=	NC_000005.10:g.150115725G>A	NC_000005.10:g.150115725G>C	NC_000005.10:g.150115725G>T
GRCh37.p13 chr 5	NC_000005.9:g.149495288=	NC_000005.9:g.149495288G>A	NC_000005.9:g.149495288G>C	NC_000005.9:g.149495288G>T
CSF1R RefSeqGene	NG_012303.2:g.2648=	NG_012303.2:g.2648C>T	NG_012303.2:g.2648C>G	NG_012303.2:g.2648C>A
PDGFRB RefSeqGene	NG_023367.1:g.45135=	NG_023367.1:g.45135C>T	NG_023367.1:g.45135C>G	NG_023367.1:g.45135C>A
PDGFRB transcript variant 1	NM_002609.4:c.*38=	NM_002609.4:c.*38C>T	NM_002609.4:c.*38C>G	NM_002609.4:c.*38C>A
PDGFRB transcript variant 1	NM_002609.3:c.*38=	NM_002609.3:c.*38C>T	NM_002609.3:c.*38C>G	NM_002609.3:c.*38C>A
PDGFRB transcript variant 3	NM_001355017.2:c.*38=	NM_001355017.2:c.*38C>T	NM_001355017.2:c.*38C>G	NM_001355017.2:c.*38C>A
PDGFRB transcript variant 3	NM_001355017.1:c.*38=	NM_001355017.1:c.*38C>T	NM_001355017.1:c.*38C>G	NM_001355017.1:c.*38C>A
PDGFRB transcript variant 2	NM_001355016.2:c.*38=	NM_001355016.2:c.*38C>T	NM_001355016.2:c.*38C>G	NM_001355016.2:c.*38C>A
PDGFRB transcript variant 2	NM_001355016.1:c.*38=	NM_001355016.1:c.*38C>T	NM_001355016.1:c.*38C>G	NM_001355016.1:c.*38C>A

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#.

25 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss488819195	May 04, 2012 (137)
2	SSMP	ss652695318	Apr 25, 2013 (138)
3	1000GENOMES	ss1317729587	Aug 21, 2014 (142)
4	EVA_UK10K_ALSPAC	ss1614287949	Apr 01, 2015 (144)
5	EVA_UK10K_TWINSUK	ss1657281982	Apr 01, 2015 (144)
6	EVA_EXAC	ss1688037676	Apr 01, 2015 (144)
7	EVA_EXAC	ss1688037677	Apr 01, 2015 (144)
8	HUMAN_LONGEVITY	ss2279232188	Dec 20, 2016 (150)
9	GNOMAD	ss2735353082	Nov 08, 2017 (151)
10	GNOMAD	ss2747488738	Nov 08, 2017 (151)
11	GNOMAD	ss2832248780	Nov 08, 2017 (151)
12	EGCUT_WGS	ss3665917425	Jul 13, 2019 (153)
13	EVA	ss3764218841	Jul 13, 2019 (153)
14	KRGDB	ss3909915575	Apr 26, 2020 (154)
15	KOGIC	ss3957889860	Apr 26, 2020 (154)
16	TOPMED	ss4683209608	Apr 26, 2021 (155)
17	TOPMED	ss4683209609	Apr 26, 2021 (155)
18	TOPMED	ss4683209610	Apr 26, 2021 (155)
19	TOMMO_GENOMICS	ss5174723763	Apr 26, 2021 (155)
20	EVA	ss5361787829	Oct 13, 2022 (156)
21	HUGCELL_USP	ss5464210938	Oct 13, 2022 (156)
22	1000G_HIGH_COVERAGE	ss5551171278	Oct 13, 2022 (156)
23	TOMMO_GENOMICS	ss5711972057	Oct 13, 2022 (156)
24	YY_MCH	ss5806873748	Oct 13, 2022 (156)
25	EVA	ss5896843543	Oct 13, 2022 (156)
26	1000Genomes	NC_000005.9 - 149495288	Oct 12, 2018 (152)
27	1000Genomes_30x	NC_000005.10 - 150115725	Oct 13, 2022 (156)
28	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 149495288	Oct 12, 2018 (152)
29	Genetic variation in the Estonian population	NC_000005.9 - 149495288	Oct 12, 2018 (152)
30	ExAC Submission ignored due to conflicting rows: Row 8047304 (NC_000005.9:149495287:G:G 99436/99470, NC_000005.9:149495287:G:C 34/99470) Row 8047305 (NC_000005.9:149495287:G:G 99464/99470, NC_000005.9:149495287:G:T 6/99470)	-	Oct 12, 2018 (152)
31	ExAC Submission ignored due to conflicting rows: Row 8047304 (NC_000005.9:149495287:G:G 99436/99470, NC_000005.9:149495287:G:C 34/99470) Row 8047305 (NC_000005.9:149495287:G:G 99464/99470, NC_000005.9:149495287:G:T 6/99470)	-	Oct 12, 2018 (152)
32	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208144035 (NC_000005.10:150115724:G:A 5/140266) Row 208144036 (NC_000005.10:150115724:G:C 11/140266) Row 208144037 (NC_000005.10:150115724:G:T 11/140266)	-	Apr 26, 2021 (155)
33	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208144035 (NC_000005.10:150115724:G:A 5/140266) Row 208144036 (NC_000005.10:150115724:G:C 11/140266) Row 208144037 (NC_000005.10:150115724:G:T 11/140266)	-	Apr 26, 2021 (155)
34	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208144035 (NC_000005.10:150115724:G:A 5/140266) Row 208144036 (NC_000005.10:150115724:G:C 11/140266) Row 208144037 (NC_000005.10:150115724:G:T 11/140266)	-	Apr 26, 2021 (155)
35	gnomAD - Exomes Submission ignored due to conflicting rows: Row 4484706 (NC_000005.9:149495287:G:G 181803/181804, NC_000005.9:149495287:G:A 1/181804) Row 4484707 (NC_000005.9:149495287:G:G 181748/181804, NC_000005.9:149495287:G:C 56/181804) Row 4484708 (NC_000005.9:149495287:G:G 181793/181804, NC_000005.9:149495287:G:T 11/181804)	-	Jul 13, 2019 (153)
36	gnomAD - Exomes Submission ignored due to conflicting rows: Row 4484706 (NC_000005.9:149495287:G:G 181803/181804, NC_000005.9:149495287:G:A 1/181804) Row 4484707 (NC_000005.9:149495287:G:G 181748/181804, NC_000005.9:149495287:G:C 56/181804) Row 4484708 (NC_000005.9:149495287:G:G 181793/181804, NC_000005.9:149495287:G:T 11/181804)	-	Jul 13, 2019 (153)
37	gnomAD - Exomes Submission ignored due to conflicting rows: Row 4484706 (NC_000005.9:149495287:G:G 181803/181804, NC_000005.9:149495287:G:A 1/181804) Row 4484707 (NC_000005.9:149495287:G:G 181748/181804, NC_000005.9:149495287:G:C 56/181804) Row 4484708 (NC_000005.9:149495287:G:G 181793/181804, NC_000005.9:149495287:G:T 11/181804)	-	Jul 13, 2019 (153)
38	KOREAN population from KRGDB	NC_000005.9 - 149495288	Apr 26, 2020 (154)
39	Korean Genome Project	NC_000005.10 - 150115725	Apr 26, 2020 (154)
40	8.3KJPN	NC_000005.9 - 149495288	Apr 26, 2021 (155)
41	14KJPN	NC_000005.10 - 150115725	Oct 13, 2022 (156)
42	TopMed Submission ignored due to conflicting rows: Row 520587165 (NC_000005.10:150115724:G:A 7/264690) Row 520587166 (NC_000005.10:150115724:G:C 23/264690) Row 520587167 (NC_000005.10:150115724:G:T 38/264690)	-	Apr 26, 2021 (155)
43	TopMed Submission ignored due to conflicting rows: Row 520587165 (NC_000005.10:150115724:G:A 7/264690) Row 520587166 (NC_000005.10:150115724:G:C 23/264690) Row 520587167 (NC_000005.10:150115724:G:T 38/264690)	-	Apr 26, 2021 (155)
44	TopMed Submission ignored due to conflicting rows: Row 520587165 (NC_000005.10:150115724:G:A 7/264690) Row 520587166 (NC_000005.10:150115724:G:C 23/264690) Row 520587167 (NC_000005.10:150115724:G:T 38/264690)	-	Apr 26, 2021 (155)
45	UK 10K study - Twins	NC_000005.9 - 149495288	Oct 12, 2018 (152)
46	ALFA	NC_000005.10 - 150115725	Apr 26, 2021 (155)

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
17092969, ss2735353082, ss2747488738, ss2832248780, ss3909915575	NC_000005.9:149495287:G:A	NC_000005.10:150115724:G:A	(self)
4413906727, ss4683209608	NC_000005.10:150115724:G:A	NC_000005.10:150115724:G:A	(self)
29426309, 17092969, 32693070, ss488819195, ss652695318, ss1317729587, ss1688037676, ss2735353082, ss2747488738, ss2832248780, ss3764218841, ss3909915575, ss5174723763, ss5361787829	NC_000005.9:149495287:G:C	NC_000005.10:150115724:G:C	(self)
38697213, 14267861, 45809161, 4413906727, ss2279232188, ss3957889860, ss4683209609, ss5464210938, ss5551171278, ss5711972057, ss5806873748, ss5896843543	NC_000005.10:150115724:G:C	NC_000005.10:150115724:G:C	(self)
16373440, 11655673, 16373440, ss1614287949, ss1657281982, ss1688037677, ss2735353082, ss2747488738, ss2832248780, ss3665917425	NC_000005.9:149495287:G:T	NC_000005.10:150115724:G:T	(self)
4413906727, ss2279232188, ss4683209610	NC_000005.10:150115724:G:T	NC_000005.10:150115724:G:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs202160957

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
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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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs202160957