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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
chr4:761233 (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=0.00015 (26/176728, GnomAD)
T=0.00002 (2/125568, TOPMED)
T=0.00014 (16/111610, ExAC) (+ 1 more)
T=0.000 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PCGF3 : Intron Variant
LOC107986211 : 5 Prime UTR 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.761233C>T
GRCh37.p13 chr 4 NC_000004.11:g.755021C>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
Gene: LOC107986211, uncharacterized LOC107986211 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107986211 transcript XM_024454317.1:c. N/A 5 Prime UTR 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
gnomAD - Exomes Global Study-wide 176728 C=0.99985 T=0.00015
gnomAD - Exomes European Sub 106202 C=0.99999 T=0.00001
gnomAD - Exomes Asian Sub 30620 C=0.9992 T=0.0008
gnomAD - Exomes American Sub 18236 C=0.9999 T=0.0001
gnomAD - Exomes African Sub 13262 C=0.9999 T=0.0001
gnomAD - Exomes Ashkenazi Jewish Sub 4950 C=1.000 T=0.000
gnomAD - Exomes Other Sub 3458 C=1.000 T=0.000
TopMed Global Study-wide 125568 C=0.99998 T=0.00002
ExAC Global Study-wide 111610 C=0.99986 T=0.00014
ExAC Europe Sub 70160 C=1.0000 T=0.0000
ExAC Asian Sub 19778 C=0.9992 T=0.0008
ExAC American Sub 11390 C=1.0000 T=0.0000
ExAC African Sub 9462 C=1.000 T=0.000
ExAC Other Sub 820 C=1.00 T=0.00
1000Genomes Global Study-wide 5008 C=1.000 T=0.000
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=1.000 T=0.000
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00

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.761233C= NC_000004.12:g.761233C>T
GRCh37.p13 chr 4 NC_000004.11:g.755021C= NC_000004.11:g.755021C>T
LOC107986211 transcript XM_024454317.1:c.-1186G= XM_024454317.1:c.-1186G>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#.

5 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1308056152 Aug 21, 2014 (142)
2 EVA_EXAC ss1687377001 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2259757044 Dec 20, 2016 (150)
4 GNOMAD ss2734327456 Nov 08, 2017 (151)
5 TOPMED ss3418003725 Nov 08, 2017 (151)
6 1000Genomes NC_000004.11 - 755021 Oct 12, 2018 (152)
7 ExAC NC_000004.11 - 755021 Oct 12, 2018 (152)
8 gnomAD - Exomes NC_000004.11 - 755021 Oct 12, 2018 (152)
9 TopMed NC_000004.12 - 761233 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
19393073, 7332068, 2723691, ss1308056152, ss1687377001, ss2734327456 NC_000004.11:755020:C= NC_000004.12:761232:C= (self)
273355296, ss2259757044, ss3418003725 NC_000004.12:761232:C= NC_000004.12:761232:C= (self)
19393073, 7332068, 2723691, ss1308056152, ss1687377001, ss2734327456 NC_000004.11:755020:C>T NC_000004.12:761232:C>T (self)
273355296, ss2259757044, ss3418003725 NC_000004.12:761232:C>T NC_000004.12:761232: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 rs536186988

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