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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.

rs5894

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr5:76732741 (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.

Alleles
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00342 (859/251486, GnomAD_exome)
G=0.00327 (410/125568, TOPMED)
G=0.00379 (460/121412, ExAC) (+ 7 more)
G=0.0037 (116/31404, GnomAD)
G=0.0037 (48/13006, GO-ESP)
G=0.002 (11/5008, 1000G)
G=0.004 (19/4480, Estonian)
G=0.006 (22/3854, ALSPAC)
G=0.005 (17/3708, TWINSUK)
G=0.01 (7/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
F2R : Synonymous Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 5 NC_000005.10:g.76732741T>G
GRCh37.p13 chr 5 NC_000005.9:g.76028566T>G
F2R RefSeqGene NG_032906.1:g.21699T>G
Gene: F2R, coagulation factor II thrombin receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
F2R transcript variant 1 NM_001992.5:c.516T>G S [TCT] > S [TCG] Coding Sequence Variant
proteinase-activated receptor 1 isoform 1 precursor NP_001983.2:p.Ser172= S (Ser) > S (Ser) Synonymous Variant
F2R transcript variant 2 NM_001311313.2:c.153T>G S [TCT] > S [TCG] Coding Sequence Variant
proteinase-activated receptor 1 isoform 2 NP_001298242.1:p.Ser51= S (Ser) > S (Ser) Synonymous 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

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
gnomAD - Exomes Global Study-wide 251486 T=0.99658 G=0.00342
gnomAD - Exomes European Sub 135410 T=0.99447 G=0.00553
gnomAD - Exomes Asian Sub 49008 T=0.9993 G=0.0007
gnomAD - Exomes American Sub 34592 T=0.9990 G=0.0010
gnomAD - Exomes African Sub 16256 T=0.9987 G=0.0013
gnomAD - Exomes Ashkenazi Jewish Sub 10080 T=1.0000 G=0.0000
gnomAD - Exomes Other Sub 6140 T=0.996 G=0.004
TopMed Global Study-wide 125568 T=0.99673 G=0.00327
ExAC Global Study-wide 121412 T=0.99621 G=0.00379
ExAC Europe Sub 73354 T=0.9943 G=0.0057
ExAC Asian Sub 25166 T=0.9993 G=0.0007
ExAC American Sub 11578 T=0.9990 G=0.0010
ExAC African Sub 10406 T=0.9988 G=0.0012
ExAC Other Sub 908 T=1.00 G=0.00
gnomAD - Genomes Global Study-wide 31404 T=0.9963 G=0.0037
gnomAD - Genomes European Sub 18904 T=0.9947 G=0.0053
gnomAD - Genomes African Sub 8716 T=0.999 G=0.001
gnomAD - Genomes East Asian Sub 1558 T=1.000 G=0.000
gnomAD - Genomes Other Sub 1088 T=0.996 G=0.004
gnomAD - Genomes American Sub 848 T=1.00 G=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13006 T=0.9963 G=0.0037
GO Exome Sequencing Project European American Sub 8600 T=0.995 G=0.005
GO Exome Sequencing Project African American Sub 4406 T=0.998 G=0.002
1000Genomes Global Study-wide 5008 T=0.998 G=0.002
1000Genomes African Sub 1322 T=0.999 G=0.001
1000Genomes East Asian Sub 1008 T=1.000 G=0.000
1000Genomes Europe Sub 1006 T=0.993 G=0.007
1000Genomes South Asian Sub 978 T=1.00 G=0.00
1000Genomes American Sub 694 T=1.00 G=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.996 G=0.004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.994 G=0.006
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.995 G=0.005
Northern Sweden ACPOP Study-wide 600 T=0.99 G=0.01
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 T= G Note
GRCh38.p12 chr 5 NC_000005.10:g.76732741= NC_000005.10:g.76732741T>G
GRCh37.p13 chr 5 NC_000005.9:g.76028566= NC_000005.9:g.76028566T>G
F2R RefSeqGene NG_032906.1:g.21699= NG_032906.1:g.21699T>G
F2R transcript variant 1 NM_001992.4:c.516= NM_001992.4:c.516T>G
F2R transcript variant 1 NM_001992.5:c.516= NM_001992.5:c.516T>G
F2R transcript NM_001992.3:c.516= NM_001992.3:c.516T>G
F2R transcript variant 2 NM_001311313.1:c.153= NM_001311313.1:c.153T>G
F2R transcript variant 2 NM_001311313.2:c.153= NM_001311313.2:c.153T>G
proteinase-activated receptor 1 isoform 1 precursor NP_001983.2:p.Ser172= NP_001983.2:p.Ser172=
proteinase-activated receptor 1 isoform 2 NP_001298242.1:p.Ser51= NP_001298242.1:p.Ser51=
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#.

58 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF-CSNP ss7496 Sep 19, 2000 (52)
2 PGA-UW-FHCRC ss3172437 Aug 15, 2001 (98)
3 PGA-UW-FHCRC ss14339391 Dec 05, 2003 (119)
4 PERLEGEN ss24676086 Sep 20, 2004 (123)
5 SEQUENOM ss24811807 Sep 20, 2004 (123)
6 SI_EXO ss52080029 Oct 16, 2006 (127)
7 ILLUMINA ss75131629 Dec 06, 2007 (129)
8 KRIBB_YJKIM ss119337711 Dec 01, 2009 (131)
9 ILLUMINA ss160748378 Dec 01, 2009 (131)
10 ILLUMINA ss173934494 Jul 04, 2010 (132)
11 1000GENOMES ss232999219 Jul 14, 2010 (132)
12 ILLUMINA ss244303708 Jul 04, 2010 (132)
13 NHLBI-ESP ss342183407 May 09, 2011 (134)
14 ILLUMINA ss481164567 May 04, 2012 (137)
15 ILLUMINA ss481186941 May 04, 2012 (137)
16 ILLUMINA ss482175011 Sep 08, 2015 (146)
17 ILLUMINA ss485377480 May 04, 2012 (137)
18 1000GENOMES ss490905469 May 04, 2012 (137)
19 CLINSEQ_SNP ss491868698 May 04, 2012 (137)
20 ILLUMINA ss537317247 Sep 08, 2015 (146)
21 ILLUMINA ss779044912 Sep 08, 2015 (146)
22 ILLUMINA ss783134309 Sep 08, 2015 (146)
23 ILLUMINA ss784090690 Sep 08, 2015 (146)
24 ILLUMINA ss832393247 Sep 08, 2015 (146)
25 ILLUMINA ss834507801 Sep 08, 2015 (146)
26 EVA-GONL ss981710826 Aug 21, 2014 (142)
27 1000GENOMES ss1315648939 Aug 21, 2014 (142)
28 HAMMER_LAB ss1397416990 Sep 08, 2015 (146)
29 EVA_FINRISK ss1584039368 Apr 01, 2015 (144)
30 EVA_DECODE ss1591230440 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1613180582 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1656174615 Apr 01, 2015 (144)
33 EVA_EXAC ss1687855300 Apr 01, 2015 (144)
34 EVA_MGP ss1711090034 Apr 01, 2015 (144)
35 ILLUMINA ss1752584826 Sep 08, 2015 (146)
36 HUMAN_LONGEVITY ss2274840912 Dec 20, 2016 (150)
37 TOPMED ss2443075478 Dec 20, 2016 (150)
38 ILLUMINA ss2634295627 Nov 08, 2017 (151)
39 GNOMAD ss2735074262 Nov 08, 2017 (151)
40 GNOMAD ss2747407097 Nov 08, 2017 (151)
41 GNOMAD ss2826230127 Nov 08, 2017 (151)
42 SWEGEN ss2997162080 Nov 08, 2017 (151)
43 TOPMED ss3468206005 Nov 08, 2017 (151)
44 ILLUMINA ss3629263696 Oct 12, 2018 (152)
45 ILLUMINA ss3632221925 Oct 12, 2018 (152)
46 ILLUMINA ss3633378583 Oct 12, 2018 (152)
47 ILLUMINA ss3634099329 Oct 12, 2018 (152)
48 ILLUMINA ss3635007466 Oct 12, 2018 (152)
49 ILLUMINA ss3635781280 Oct 12, 2018 (152)
50 ILLUMINA ss3636719613 Oct 12, 2018 (152)
51 ILLUMINA ss3637533905 Oct 12, 2018 (152)
52 ILLUMINA ss3638561072 Oct 12, 2018 (152)
53 ILLUMINA ss3640714759 Oct 12, 2018 (152)
54 ILLUMINA ss3643506565 Oct 12, 2018 (152)
55 EGCUT_WGS ss3665040770 Jul 13, 2019 (153)
56 ACPOP ss3732475679 Jul 13, 2019 (153)
57 ILLUMINA ss3745307679 Jul 13, 2019 (153)
58 ILLUMINA ss3772801822 Jul 13, 2019 (153)
59 1000Genomes NC_000005.9 - 76028566 Oct 12, 2018 (152)
60 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 76028566 Oct 12, 2018 (152)
61 Genetic variation in the Estonian population NC_000005.9 - 76028566 Oct 12, 2018 (152)
62 ExAC NC_000005.9 - 76028566 Oct 12, 2018 (152)
63 gnomAD - Genomes NC_000005.9 - 76028566 Jul 13, 2019 (153)
64 gnomAD - Exomes NC_000005.9 - 76028566 Jul 13, 2019 (153)
65 GO Exome Sequencing Project NC_000005.9 - 76028566 Oct 12, 2018 (152)
66 Northern Sweden NC_000005.9 - 76028566 Jul 13, 2019 (153)
67 TopMed NC_000005.10 - 76732741 Oct 12, 2018 (152)
68 UK 10K study - Twins NC_000005.9 - 76028566 Oct 12, 2018 (152)
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).

Associated ID History Updated (Build)
rs17568474 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss481164567, ss491868698, ss1397416990, ss1591230440, ss3643506565 NC_000005.8:76064321:T:G NC_000005.10:76732740:T:G (self)
27269158, 15161277, 10779018, 7850427, 74514581, 4193235, 550124, 5760544, 15161277, ss232999219, ss342183407, ss481186941, ss482175011, ss485377480, ss490905469, ss537317247, ss779044912, ss783134309, ss784090690, ss832393247, ss834507801, ss981710826, ss1315648939, ss1584039368, ss1613180582, ss1656174615, ss1687855300, ss1711090034, ss1752584826, ss2443075478, ss2634295627, ss2735074262, ss2747407097, ss2826230127, ss2997162080, ss3629263696, ss3632221925, ss3633378583, ss3634099329, ss3635007466, ss3635781280, ss3636719613, ss3637533905, ss3638561072, ss3640714759, ss3665040770, ss3732475679, ss3745307679, ss3772801822 NC_000005.9:76028565:T:G NC_000005.10:76732740:T:G (self)
313970807, ss2274840912, ss3468206005 NC_000005.10:76732740:T:G NC_000005.10:76732740:T:G (self)
ss52080029 NT_006713.14:26622923:T:G NC_000005.10:76732740:T:G (self)
ss7496, ss3172437, ss14339391, ss24676086, ss24811807, ss75131629, ss119337711, ss160748378, ss173934494, ss244303708 NT_006713.15:26622924:T:G NC_000005.10:76732740:T:G (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 rs5894

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.post270+ab078da