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dbSNP Short Genetic Variations

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.


Current Build 152

Released October 2, 2018

Homo sapiens
chr4:736167 (GRCh38.p12) 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.

Variation Type
SNV Single Nucleotide Variation
T=0.00424 (532/125568, TOPMED)
T=0.0036 (112/30930, GnomAD)
T=0.001 (6/5008, 1000G) (+ 1 more)
T=0.002 (10/4480, Estonian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PCGF3 : Intron Variant
0 citations
Genomic View
See rs on genome

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.p12 chr 4 NC_000004.12:g.736167C>T
GRCh37.p13 chr 4 NC_000004.11:g.729956C>T
Gene: PCGF3, polycomb group ring finger 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PCGF3 transcript variant 1 NM_001317836.1:c. N/A Intron Variant
PCGF3 transcript variant 2 NM_006315.5:c. N/A Intron 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

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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.99576 T=0.00424
gnomAD - Genomes Global Study-wide 30930 C=0.9964 T=0.0036
gnomAD - Genomes European Sub 18470 C=0.9950 T=0.0050
gnomAD - Genomes African Sub 8720 C=0.999 T=0.001
gnomAD - Genomes East Asian Sub 1622 C=1.000 T=0.000
gnomAD - Genomes Other Sub 982 C=0.99 T=0.01
gnomAD - Genomes American Sub 838 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 298 C=1.00 T=0.00
1000Genomes Global Study-wide 5008 C=0.999 T=0.001
1000Genomes African Sub 1322 C=1.000 T=0.000
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.997 T=0.003
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.998 T=0.002

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 Note
GRCh38.p12 chr 4 NC_000004.12:g.736167C= NC_000004.12:g.736167C>T
GRCh37.p13 chr 4 NC_000004.11:g.729956C= NC_000004.11:g.729956C>T

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#.

10 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss456821238 Sep 17, 2011 (135)
2 EVA-GONL ss979664525 Aug 21, 2014 (142)
3 1000GENOMES ss1308055152 Aug 21, 2014 (142)
4 EVA_DECODE ss1589161496 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2259755152 Dec 20, 2016 (150)
6 TOPMED ss2427153888 Dec 20, 2016 (150)
7 GNOMAD ss2804592537 Nov 08, 2017 (151)
8 SWEGEN ss2993978841 Nov 08, 2017 (151)
9 CSHL ss3345494064 Nov 08, 2017 (151)
10 TOPMED ss3417997396 Nov 08, 2017 (151)
11 1000Genomes NC_000004.11 - 729956 Oct 12, 2018 (152)
12 Genetic variation in the Estonian population NC_000004.11 - 729956 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000004.11 - 729956 Oct 12, 2018 (152)
14 TopMed NC_000004.12 - 736167 Oct 12, 2018 (152)

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
ss1589161496 NC_000004.10:719955:C= NC_000004.12:736166:C= (self)
19392044, 7656219, 145220292, ss456821238, ss979664525, ss1308055152, ss2427153888, ss2804592537, ss2993978841, ss3345494064 NC_000004.11:729955:C= NC_000004.12:736166:C= (self)
273350968, ss2259755152, ss3417997396 NC_000004.12:736166:C= NC_000004.12:736166:C= (self)
ss1589161496 NC_000004.10:719955:C>T NC_000004.12:736166:C>T (self)
19392044, 7656219, 145220292, ss456821238, ss979664525, ss1308055152, ss2427153888, ss2804592537, ss2993978841, ss3345494064 NC_000004.11:729955:C>T NC_000004.12:736166:C>T (self)
273350968, ss2259755152, ss3417997396 NC_000004.12:736166:C>T NC_000004.12:736166:C>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 rs180711823

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.post104+4a6ee9c