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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.

rs61731861

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:11650003 (GRCh38.p13) 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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.002565 (679/264690, TOPMED)
C=0.003221 (809/251196, GnomAD_exome)
C=0.002681 (376/140264, GnomAD) (+ 11 more)
C=0.003581 (434/121208, ExAC)
C=0.003774 (448/118708, ALFA)
C=0.00006 (1/16760, 8.3KJPN)
C=0.00377 (49/13006, GO-ESP)
C=0.0020 (10/5008, 1000G)
C=0.0022 (10/4480, Estonian)
C=0.0042 (16/3854, ALSPAC)
C=0.0046 (17/3708, TWINSUK)
C=0.0003 (1/2922, KOREAN)
C=0.009 (9/998, GoNL)
C=0.002 (1/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FBXO2 : Missense 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.p13 chr 1 NC_000001.11:g.11650003T>A
GRCh38.p13 chr 1 NC_000001.11:g.11650003T>C
GRCh37.p13 chr 1 NC_000001.10:g.11710060T>A
GRCh37.p13 chr 1 NC_000001.10:g.11710060T>C
Gene: FBXO2, F-box protein 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FBXO2 transcript NM_012168.6:c.463A>T S [AGT] > C [TGT] Coding Sequence Variant
F-box only protein 2 NP_036300.2:p.Ser155Cys S (Ser) > C (Cys) Missense Variant
FBXO2 transcript NM_012168.6:c.463A>G S [AGT] > G [GGT] Coding Sequence Variant
F-box only protein 2 NP_036300.2:p.Ser155Gly S (Ser) > G (Gly) 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 118708 T=0.996226 A=0.000000, C=0.003774
European Sub 95482 T=0.99578 A=0.00000, C=0.00422
African Sub 4108 T=0.9995 A=0.0000, C=0.0005
African Others Sub 124 T=1.000 A=0.000, C=0.000
African American Sub 3984 T=0.9995 A=0.0000, C=0.0005
Asian Sub 3162 T=1.0000 A=0.0000, C=0.0000
East Asian Sub 1928 T=1.0000 A=0.0000, C=0.0000
Other Asian Sub 1234 T=1.0000 A=0.0000, C=0.0000
Latin American 1 Sub 500 T=1.000 A=0.000, C=0.000
Latin American 2 Sub 648 T=1.000 A=0.000, C=0.000
South Asian Sub 104 T=1.000 A=0.000, C=0.000
Other Sub 14704 T=0.99708 A=0.00000, C=0.00292


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 T=0.997435 C=0.002565
gnomAD - Exomes Global Study-wide 251196 T=0.996779 C=0.003221
gnomAD - Exomes European Sub 135174 T=0.995436 C=0.004564
gnomAD - Exomes Asian Sub 49006 T=0.99806 C=0.00194
gnomAD - Exomes American Sub 34574 T=0.99850 C=0.00150
gnomAD - Exomes African Sub 16238 T=0.99901 C=0.00099
gnomAD - Exomes Ashkenazi Jewish Sub 10068 T=0.99891 C=0.00109
gnomAD - Exomes Other Sub 6136 T=0.9971 C=0.0029
gnomAD - Genomes Global Study-wide 140264 T=0.997319 C=0.002681
gnomAD - Genomes European Sub 75956 T=0.99588 C=0.00412
gnomAD - Genomes African Sub 42052 T=0.99907 C=0.00093
gnomAD - Genomes American Sub 13646 T=0.99853 C=0.00147
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9991 C=0.0009
gnomAD - Genomes East Asian Sub 3132 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 T=0.9995 C=0.0005
ExAC Global Study-wide 121208 T=0.996419 C=0.003581
ExAC Europe Sub 73256 T=0.99514 C=0.00486
ExAC Asian Sub 25146 T=0.99793 C=0.00207
ExAC American Sub 11560 T=0.99913 C=0.00087
ExAC African Sub 10340 T=0.99874 C=0.00126
ExAC Other Sub 906 T=0.997 C=0.003
8.3KJPN JAPANESE Study-wide 16760 T=0.99994 C=0.00006
GO Exome Sequencing Project Global Study-wide 13006 T=0.99623 C=0.00377
GO Exome Sequencing Project European American Sub 8600 T=0.9952 C=0.0048
GO Exome Sequencing Project African American Sub 4406 T=0.9982 C=0.0018
1000Genomes Global Study-wide 5008 T=0.9980 C=0.0020
1000Genomes African Sub 1322 T=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9970 C=0.0030
1000Genomes South Asian Sub 978 T=0.993 C=0.007
1000Genomes American Sub 694 T=1.000 C=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9978 C=0.0022
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9958 C=0.0042
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9954 C=0.0046
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9997 C=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.991 C=0.009
Northern Sweden ACPOP Study-wide 600 T=0.998 C=0.002
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= A C
GRCh38.p13 chr 1 NC_000001.11:g.11650003= NC_000001.11:g.11650003T>A NC_000001.11:g.11650003T>C
GRCh37.p13 chr 1 NC_000001.10:g.11710060= NC_000001.10:g.11710060T>A NC_000001.10:g.11710060T>C
FBXO2 transcript NM_012168.6:c.463= NM_012168.6:c.463A>T NM_012168.6:c.463A>G
FBXO2 transcript NM_012168.5:c.463= NM_012168.5:c.463A>T NM_012168.5:c.463A>G
F-box only protein 2 NP_036300.2:p.Ser155= NP_036300.2:p.Ser155Cys NP_036300.2:p.Ser155Gly
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#.

44 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 CORNELL ss86244033 Mar 23, 2008 (129)
2 1000GENOMES ss217410513 Jul 14, 2010 (132)
3 NHLBI-ESP ss341932883 May 09, 2011 (134)
4 1000GENOMES ss488651933 May 04, 2012 (137)
5 EXOME_CHIP ss491286196 May 04, 2012 (137)
6 CLINSEQ_SNP ss491584485 May 04, 2012 (137)
7 ILLUMINA ss780747699 Aug 21, 2014 (142)
8 ILLUMINA ss783425533 Aug 21, 2014 (142)
9 EVA-GONL ss974858974 Aug 21, 2014 (142)
10 1000GENOMES ss1289696554 Aug 21, 2014 (142)
11 EVA_DECODE ss1584217167 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1599555186 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1642549219 Apr 01, 2015 (144)
14 EVA_EXAC ss1685301750 Apr 01, 2015 (144)
15 ILLUMINA ss1751865782 Sep 08, 2015 (146)
16 ILLUMINA ss1917722667 Feb 12, 2016 (147)
17 ILLUMINA ss1945984696 Feb 12, 2016 (147)
18 ILLUMINA ss1958241446 Feb 12, 2016 (147)
19 JJLAB ss2019543200 Sep 14, 2016 (149)
20 HUMAN_LONGEVITY ss2160076990 Dec 20, 2016 (150)
21 TOPMED ss2322234695 Dec 20, 2016 (150)
22 GNOMAD ss2731117091 Nov 08, 2017 (151)
23 GNOMAD ss2746214283 Nov 08, 2017 (151)
24 GNOMAD ss2751661206 Nov 08, 2017 (151)
25 AFFY ss2984845247 Nov 08, 2017 (151)
26 SWEGEN ss2986301566 Nov 08, 2017 (151)
27 ILLUMINA ss3021054491 Nov 08, 2017 (151)
28 TOPMED ss3068682756 Nov 08, 2017 (151)
29 TOPMED ss3068682757 Nov 08, 2017 (151)
30 ILLUMINA ss3634306930 Oct 11, 2018 (152)
31 ILLUMINA ss3640014294 Oct 11, 2018 (152)
32 ILLUMINA ss3644480550 Oct 11, 2018 (152)
33 ILLUMINA ss3651378439 Oct 11, 2018 (152)
34 ILLUMINA ss3653618879 Oct 11, 2018 (152)
35 EGCUT_WGS ss3654402316 Jul 12, 2019 (153)
36 ILLUMINA ss3724996587 Jul 12, 2019 (153)
37 ACPOP ss3726793110 Jul 12, 2019 (153)
38 ILLUMINA ss3744339275 Jul 12, 2019 (153)
39 ILLUMINA ss3744607912 Jul 12, 2019 (153)
40 ILLUMINA ss3772109524 Jul 12, 2019 (153)
41 EVA ss3823559787 Apr 25, 2020 (154)
42 KRGDB ss3893085771 Apr 25, 2020 (154)
43 TOPMED ss4439338615 Apr 25, 2021 (155)
44 TOMMO_GENOMICS ss5142492446 Apr 25, 2021 (155)
45 1000Genomes NC_000001.10 - 11710060 Oct 11, 2018 (152)
46 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 11710060 Oct 11, 2018 (152)
47 Genetic variation in the Estonian population NC_000001.10 - 11710060 Oct 11, 2018 (152)
48 ExAC NC_000001.10 - 11710060 Oct 11, 2018 (152)
49 gnomAD - Genomes NC_000001.11 - 11650003 Apr 25, 2021 (155)
50 gnomAD - Exomes NC_000001.10 - 11710060 Jul 12, 2019 (153)
51 GO Exome Sequencing Project NC_000001.10 - 11710060 Oct 11, 2018 (152)
52 Genome of the Netherlands Release 5 NC_000001.10 - 11710060 Apr 25, 2020 (154)
53 KOREAN population from KRGDB NC_000001.10 - 11710060 Apr 25, 2020 (154)
54 Northern Sweden NC_000001.10 - 11710060 Jul 12, 2019 (153)
55 8.3KJPN NC_000001.10 - 11710060 Apr 25, 2021 (155)
56 TopMed NC_000001.11 - 11650003 Apr 25, 2021 (155)
57 UK 10K study - Twins NC_000001.10 - 11710060 Oct 11, 2018 (152)
58 ALFA NC_000001.11 - 11650003 Apr 25, 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
1852954, 7771361824, ss3068682756 NC_000001.11:11650002:T:A NC_000001.11:11650002:T:A (self)
ss217410513, ss491584485, ss1584217167 NC_000001.9:11632646:T:C NC_000001.11:11650002:T:C (self)
373086, 194330, 140564, 4481020, 133427, 18515, 82798, 263165, 77975, 461753, 194330, ss341932883, ss488651933, ss491286196, ss780747699, ss783425533, ss974858974, ss1289696554, ss1599555186, ss1642549219, ss1685301750, ss1751865782, ss1917722667, ss1945984696, ss1958241446, ss2019543200, ss2322234695, ss2731117091, ss2746214283, ss2751661206, ss2984845247, ss2986301566, ss3021054491, ss3634306930, ss3640014294, ss3644480550, ss3651378439, ss3653618879, ss3654402316, ss3726793110, ss3744339275, ss3744607912, ss3772109524, ss3823559787, ss3893085771, ss5142492446 NC_000001.10:11710059:T:C NC_000001.11:11650002:T:C (self)
2597248, 1852954, 2944950, 7771361824, ss2160076990, ss3068682757, ss3724996587, ss4439338615 NC_000001.11:11650002:T:C NC_000001.11:11650002:T:C (self)
ss86244033 NT_021937.19:7714791:T:C NC_000001.11:11650002:T: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 rs61731861

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.post596+ae089ad