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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
chr3:46373484 (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=0.0296 (384/12980, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CCR5 : Missense Variant
LOC102724297 : 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 3 NC_000003.12:g.46373484G>T
GRCh37.p13 chr 3 NC_000003.11:g.46414975G>T
CCR5 RefSeqGene NG_012637.1:g.8343G>T
Gene: CCR5, C-C motif chemokine receptor 5 (gene/pseudogene) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CCR5 transcript variant B NM_001100168.1:c.582G>T Q [CAG] > H [CAT] Coding Sequence Variant
C-C chemokine receptor type 5 NP_001093638.1:p.Gln194His Q (Gln) > H (His) Missense Variant
CCR5 transcript variant A NM_000579.3:c.582G>T Q [CAG] > H [CAT] Coding Sequence Variant
C-C chemokine receptor type 5 NP_000570.1:p.Gln194His Q (Gln) > H (His) Missense Variant
Gene: LOC102724297, uncharacterized LOC102724297 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CCR5AS transcript NR_125406.1:n. 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
GO Exome Sequencing Project Global Study-wide 12980 G=0.9704 T=0.0296
GO Exome Sequencing Project European American Sub 8574 G=0.961 T=0.039
GO Exome Sequencing Project African American Sub 4406 G=0.989 T=0.011

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= T Note
GRCh38.p12 chr 3 NC_000003.12:g.46373484G= NC_000003.12:g.46373484G>T
GRCh37.p13 chr 3 NC_000003.11:g.46414975G= NC_000003.11:g.46414975G>T
CCR5 RefSeqGene NG_012637.1:g.8343G= NG_012637.1:g.8343G>T
CCR5 transcript variant A NM_000579.3:c.582G= NM_000579.3:c.582G>T
CCR5 transcript variant B NM_001100168.1:c.582G= NM_001100168.1:c.582G>T
C-C chemokine receptor type 5 NP_000570.1:p.Gln194= NP_000570.1:p.Gln194His
C-C chemokine receptor type 5 NP_001093638.1:p.Gln194= NP_001093638.1:p.Gln194His

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#.

29 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss95214655 Mar 25, 2008 (129)
2 1000GENOMES ss330665584 May 09, 2011 (134)
3 1000GENOMES ss489875083 May 04, 2012 (137)
4 EXOME_CHIP ss491338710 May 04, 2012 (137)
5 ILLUMINA ss533151258 Sep 08, 2015 (146)
6 NHLBI-ESP ss712514284 Apr 25, 2013 (138)
7 ILLUMINA ss780815978 Sep 08, 2015 (146)
8 ILLUMINA ss783498160 Sep 08, 2015 (146)
9 EVA_MGP ss1711015385 Apr 01, 2015 (144)
10 ILLUMINA ss1752471724 Sep 08, 2015 (146)
11 ILLUMINA ss1917766156 Feb 12, 2016 (147)
12 WEILL_CORNELL_DGM ss1921791660 Feb 12, 2016 (147)
13 ILLUMINA ss1946081401 Feb 12, 2016 (147)
14 ILLUMINA ss1958559368 Feb 12, 2016 (147)
15 ILLUMINA ss2094927153 Dec 20, 2016 (150)
16 ILLUMINA ss2095129520 Dec 20, 2016 (150)
17 USC_VALOUEV ss2149525656 Dec 20, 2016 (150)
18 HUMAN_LONGEVITY ss2251182126 Dec 20, 2016 (150)
19 AFFY ss2985254172 Nov 08, 2017 (151)
20 ILLUMINA ss3022235376 Nov 08, 2017 (151)
21 TOPMED ss3389293289 Nov 08, 2017 (151)
22 ILLUMINA ss3628649563 Oct 12, 2018 (152)
23 ILLUMINA ss3628649564 Oct 12, 2018 (152)
24 ILLUMINA ss3634892388 Oct 12, 2018 (152)
25 ILLUMINA ss3640599690 Oct 12, 2018 (152)
26 ILLUMINA ss3644813966 Oct 12, 2018 (152)
27 ILLUMINA ss3652705993 Oct 12, 2018 (152)
28 ILLUMINA ss3652705994 Oct 12, 2018 (152)
29 ILLUMINA ss3654023176 Oct 12, 2018 (152)
30 GO Exome Sequencing Project NC_000003.11 - 46414975 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
ss2094927153 NC_000003.10:46389978:G:T NC_000003.12:46373483:G:T (self)
363443, ss330665584, ss489875083, ss491338710, ss533151258, ss712514284, ss780815978, ss783498160, ss1711015385, ss1752471724, ss1917766156, ss1921791660, ss1946081401, ss1958559368, ss2095129520, ss2149525656, ss2985254172, ss3022235376, ss3628649563, ss3628649564, ss3634892388, ss3640599690, ss3644813966, ss3652705993, ss3652705994, ss3654023176 NC_000003.11:46414974:G:T NC_000003.12:46373483:G:T (self)
ss2251182126, ss3389293289 NC_000003.12:46373483:G:T NC_000003.12:46373483:G:T (self)
ss95214655 NT_022517.18:46354974:G:T NC_000003.12:46373483: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 rs62625034

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