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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.

rs371249995

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:88074926 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000011 (3/264690, TOPMED)
A=0.000024 (6/251120, GnomAD_exome)
A=0.000014 (2/140256, GnomAD) (+ 3 more)
A=0.000016 (2/121284, ExAC)
A=0.00003 (1/35420, ALFA)
A=0.00008 (1/13006, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PKD2 : 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 51782 G=0.99996 A=0.00004
European Sub 36668 G=0.99995 A=0.00005
African Sub 7756 G=1.0000 A=0.0000
African Others Sub 298 G=1.000 A=0.000
African American Sub 7458 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 498 G=1.000 A=0.000
Latin American 2 Sub 628 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 6022 G=1.0000 A=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 G=0.999989 A=0.000011
gnomAD - Exomes Global Study-wide 251120 G=0.999976 A=0.000024
gnomAD - Exomes European Sub 135090 G=0.999963 A=0.000037
gnomAD - Exomes Asian Sub 49002 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34586 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16254 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10064 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6124 G=0.9998 A=0.0002
gnomAD - Genomes Global Study-wide 140256 G=0.999986 A=0.000014
gnomAD - Genomes European Sub 75936 G=0.99997 A=0.00003
gnomAD - Genomes African Sub 42050 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13662 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
ExAC Global Study-wide 121284 G=0.999984 A=0.000016
ExAC Europe Sub 73284 G=0.99997 A=0.00003
ExAC Asian Sub 25154 G=1.00000 A=0.00000
ExAC American Sub 11570 G=1.00000 A=0.00000
ExAC African Sub 10368 G=1.00000 A=0.00000
ExAC Other Sub 908 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 35420 G=0.99997 A=0.00003
Allele Frequency Aggregator European Sub 26578 G=0.99996 A=0.00004
Allele Frequency Aggregator Other Sub 4588 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2918 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 498 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
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 4 NC_000004.12:g.88074926G>A
GRCh38.p14 chr 4 NC_000004.12:g.88074926G>C
GRCh37.p13 chr 4 NC_000004.11:g.88996078G>A
GRCh37.p13 chr 4 NC_000004.11:g.88996078G>C
PKD2 RefSeqGene NG_008604.1:g.72259G>A
PKD2 RefSeqGene NG_008604.1:g.72259G>C
Gene: PKD2, polycystin 2, transient receptor potential cation channel (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PKD2 transcript variant 1 NM_000297.4:c.2637G>A E [GAG] > E [GAA] Coding Sequence Variant
polycystin-2 NP_000288.1:p.Glu879= E (Glu) > E (Glu) Synonymous Variant
PKD2 transcript variant 1 NM_000297.4:c.2637G>C E [GAG] > D [GAC] Coding Sequence Variant
polycystin-2 NP_000288.1:p.Glu879Asp E (Glu) > D (Asp) Missense Variant
PKD2 transcript variant 2 NR_156488.2:n.2615G>A N/A Non Coding Transcript Variant
PKD2 transcript variant 2 NR_156488.2:n.2615G>C N/A Non Coding Transcript Variant
PKD2 transcript variant X1 XM_011532028.3:c.2412G>A E [GAG] > E [GAA] Coding Sequence Variant
polycystin-2 isoform X1 XP_011530330.1:p.Glu804= E (Glu) > E (Glu) Synonymous Variant
PKD2 transcript variant X1 XM_011532028.3:c.2412G>C E [GAG] > D [GAC] Coding Sequence Variant
polycystin-2 isoform X1 XP_011530330.1:p.Glu804Asp E (Glu) > D (Asp) Missense Variant
PKD2 transcript variant X2 XM_011532029.2:c.1917G>A E [GAG] > E [GAA] Coding Sequence Variant
polycystin-2 isoform X2 XP_011530331.1:p.Glu639= E (Glu) > E (Glu) Synonymous Variant
PKD2 transcript variant X2 XM_011532029.2:c.1917G>C E [GAG] > D [GAC] Coding Sequence Variant
polycystin-2 isoform X2 XP_011530331.1:p.Glu639Asp E (Glu) > D (Asp) Missense Variant
PKD2 transcript variant X3 XM_011532030.3:c.1797G>A E [GAG] > E [GAA] Coding Sequence Variant
polycystin-2 isoform X3 XP_011530332.1:p.Glu599= E (Glu) > E (Glu) Synonymous Variant
PKD2 transcript variant X3 XM_011532030.3:c.1797G>C E [GAG] > D [GAC] Coding Sequence Variant
polycystin-2 isoform X3 XP_011530332.1:p.Glu599Asp E (Glu) > D (Asp) 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 G= A C
GRCh38.p14 chr 4 NC_000004.12:g.88074926= NC_000004.12:g.88074926G>A NC_000004.12:g.88074926G>C
GRCh37.p13 chr 4 NC_000004.11:g.88996078= NC_000004.11:g.88996078G>A NC_000004.11:g.88996078G>C
PKD2 RefSeqGene NG_008604.1:g.72259= NG_008604.1:g.72259G>A NG_008604.1:g.72259G>C
PKD2 transcript variant 1 NM_000297.4:c.2637= NM_000297.4:c.2637G>A NM_000297.4:c.2637G>C
PKD2 transcript variant 1 NM_000297.3:c.2637= NM_000297.3:c.2637G>A NM_000297.3:c.2637G>C
PKD2 transcript variant 2 NR_156488.2:n.2615= NR_156488.2:n.2615G>A NR_156488.2:n.2615G>C
PKD2 transcript variant 2 NR_156488.1:n.2603= NR_156488.1:n.2603G>A NR_156488.1:n.2603G>C
PKD2 transcript variant X1 XM_011532028.3:c.2412= XM_011532028.3:c.2412G>A XM_011532028.3:c.2412G>C
PKD2 transcript variant X1 XM_011532028.2:c.2412= XM_011532028.2:c.2412G>A XM_011532028.2:c.2412G>C
PKD2 transcript variant X1 XM_011532028.1:c.2412= XM_011532028.1:c.2412G>A XM_011532028.1:c.2412G>C
PKD2 transcript variant X3 XM_011532030.3:c.1797= XM_011532030.3:c.1797G>A XM_011532030.3:c.1797G>C
PKD2 transcript variant X3 XM_011532030.2:c.1797= XM_011532030.2:c.1797G>A XM_011532030.2:c.1797G>C
PKD2 transcript variant X3 XM_011532030.1:c.1797= XM_011532030.1:c.1797G>A XM_011532030.1:c.1797G>C
PKD2 transcript variant X2 XM_011532029.2:c.1917= XM_011532029.2:c.1917G>A XM_011532029.2:c.1917G>C
PKD2 transcript variant X2 XM_011532029.1:c.1917= XM_011532029.1:c.1917G>A XM_011532029.1:c.1917G>C
polycystin-2 NP_000288.1:p.Glu879= NP_000288.1:p.Glu879= NP_000288.1:p.Glu879Asp
polycystin-2 isoform X1 XP_011530330.1:p.Glu804= XP_011530330.1:p.Glu804= XP_011530330.1:p.Glu804Asp
polycystin-2 isoform X3 XP_011530332.1:p.Glu599= XP_011530332.1:p.Glu599= XP_011530332.1:p.Glu599Asp
polycystin-2 isoform X2 XP_011530331.1:p.Glu639= XP_011530331.1:p.Glu639= XP_011530331.1:p.Glu639Asp
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#.

8 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712606024 Apr 25, 2013 (138)
2 EVA_EXAC ss1687569413 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2264758555 Dec 20, 2016 (150)
4 GNOMAD ss2734626252 Nov 08, 2017 (151)
5 GNOMAD ss2747272066 Nov 08, 2017 (151)
6 GNOMAD ss2811948617 Nov 08, 2017 (151)
7 EVA ss3824032016 Apr 26, 2020 (154)
8 TOPMED ss4621841765 Apr 26, 2021 (155)
9 ExAC NC_000004.11 - 88996078 Oct 12, 2018 (152)
10 gnomAD - Genomes NC_000004.12 - 88074926 Apr 26, 2021 (155)
11 gnomAD - Exomes NC_000004.11 - 88996078 Jul 13, 2019 (153)
12 GO Exome Sequencing Project NC_000004.11 - 88996078 Oct 12, 2018 (152)
13 TopMed NC_000004.12 - 88074926 Apr 26, 2021 (155)
14 ALFA NC_000004.12 - 88074926 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
7540292, 3733116, 490218, ss712606024, ss1687569413, ss2734626252, ss2747272066, ss2811948617, ss3824032016 NC_000004.11:88996077:G:A NC_000004.12:88074925:G:A (self)
156505888, 459219321, 6122940645, ss4621841765 NC_000004.12:88074925:G:A NC_000004.12:88074925:G:A (self)
ss2264758555 NC_000004.12:88074925:G:C NC_000004.12:88074925:G:C (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 rs371249995

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