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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.

rs2232032

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr14:74356940 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.006056 (1603/264690, TOPMED)
T=0.001268 (318/250858, GnomAD_exome)
T=0.000546 (106/194086, ALFA) (+ 9 more)
T=0.005563 (780/140216, GnomAD)
T=0.001702 (206/121068, ExAC)
T=0.00623 (81/13006, GO-ESP)
T=0.0056 (28/5008, 1000G)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.0149 (19/1278, HapMap)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
VRTN : 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 14 NC_000014.9:g.74356940C>T
GRCh37.p13 chr 14 NC_000014.8:g.74823643C>T
Gene: VRTN, vertebrae development associated (plus strand)
Molecule type Change Amino acid[Codon] SO Term
VRTN transcript NM_018228.3:c.157C>T L [CTC] > F [TTC] Coding Sequence Variant
vertnin NP_060698.2:p.Leu53Phe L (Leu) > F (Phe) Missense Variant
VRTN transcript variant X1 XM_011536911.2:c.157C>T L [CTC] > F [TTC] Coding Sequence Variant
vertnin isoform X1 XP_011535213.1:p.Leu53Phe L (Leu) > F (Phe) 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 (New)
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 194086 C=0.999454 T=0.000546
European Sub 163830 C=0.999921 T=0.000079
African Sub 6078 C=0.9875 T=0.0125
African Others Sub 206 C=0.995 T=0.005
African American Sub 5872 C=0.9872 T=0.0128
Asian Sub 6350 C=1.0000 T=0.0000
East Asian Sub 4502 C=1.0000 T=0.0000
Other Asian Sub 1848 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=0.994 T=0.006
Latin American 2 Sub 968 C=0.999 T=0.001
South Asian Sub 280 C=1.000 T=0.000
Other Sub 15784 C=0.99930 T=0.00070


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 C=0.993944 T=0.006056
gnomAD - Exomes Global Study-wide 250858 C=0.998732 T=0.001268
gnomAD - Exomes European Sub 134864 C=0.999963 T=0.000037
gnomAD - Exomes Asian Sub 48984 C=0.99998 T=0.00002
gnomAD - Exomes American Sub 34570 C=0.99893 T=0.00107
gnomAD - Exomes African Sub 16254 C=0.98333 T=0.01667
gnomAD - Exomes Ashkenazi Jewish Sub 10062 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6124 C=0.9993 T=0.0007
gnomAD - Genomes Global Study-wide 140216 C=0.994437 T=0.005563
gnomAD - Genomes European Sub 75936 C=0.99992 T=0.00008
gnomAD - Genomes African Sub 42022 C=0.98272 T=0.01728
gnomAD - Genomes American Sub 13652 C=0.99744 T=0.00256
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9940 T=0.0060
ExAC Global Study-wide 121068 C=0.998298 T=0.001702
ExAC Europe Sub 73182 C=0.99996 T=0.00004
ExAC Asian Sub 25010 C=1.00000 T=0.00000
ExAC American Sub 11574 C=0.99888 T=0.00112
ExAC African Sub 10396 C=0.98172 T=0.01828
ExAC Other Sub 906 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99377 T=0.00623
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9816 T=0.0184
1000Genomes Global Study-wide 5008 C=0.9944 T=0.0056
1000Genomes African Sub 1322 C=0.9811 T=0.0189
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.996 T=0.004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 T=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 T=0.0000
HapMap Global Study-wide 1278 C=0.9851 T=0.0149
HapMap African Sub 686 C=0.983 T=0.017
HapMap American Sub 420 C=0.986 T=0.014
HapMap Asian Sub 172 C=0.994 T=0.006
SGDP_PRJ Global Study-wide 2 C=0.5 T=0.5
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 C= T
GRCh38.p13 chr 14 NC_000014.9:g.74356940= NC_000014.9:g.74356940C>T
GRCh37.p13 chr 14 NC_000014.8:g.74823643= NC_000014.8:g.74823643C>T
VRTN transcript NM_018228.3:c.157= NM_018228.3:c.157C>T
VRTN transcript NM_018228.2:c.157= NM_018228.2:c.157C>T
VRTN transcript variant X1 XM_011536911.2:c.157= XM_011536911.2:c.157C>T
vertnin NP_060698.2:p.Leu53= NP_060698.2:p.Leu53Phe
vertnin isoform X1 XP_011535213.1:p.Leu53= XP_011535213.1:p.Leu53Phe
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#.

49 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 GENAISSANCE ss3179289 Aug 15, 2001 (98)
2 PERLEGEN ss69162116 May 17, 2007 (127)
3 ILLUMINA ss74855126 Dec 06, 2007 (129)
4 SEATTLESEQ ss159729625 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss169936670 Jul 04, 2010 (132)
6 ILLUMINA ss173195650 Jul 04, 2010 (132)
7 1000GENOMES ss211539163 Jul 14, 2010 (132)
8 NHLBI-ESP ss342391774 May 09, 2011 (134)
9 1000GENOMES ss463899356 Sep 17, 2011 (135)
10 1000GENOMES ss491072435 May 04, 2012 (137)
11 EXOME_CHIP ss491487299 May 04, 2012 (137)
12 CLINSEQ_SNP ss491690375 May 04, 2012 (137)
13 ILLUMINA ss537057968 Sep 08, 2015 (146)
14 TISHKOFF ss564187723 Apr 25, 2013 (138)
15 ILLUMINA ss780703052 Sep 08, 2015 (146)
16 ILLUMINA ss783377412 Sep 08, 2015 (146)
17 JMKIDD_LAB ss1067547127 Aug 21, 2014 (142)
18 1000GENOMES ss1351634028 Aug 21, 2014 (142)
19 EVA_UK10K_ALSPAC ss1632076168 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1675070201 Apr 01, 2015 (144)
21 EVA_EXAC ss1691556464 Apr 01, 2015 (144)
22 ILLUMINA ss1752141929 Sep 08, 2015 (146)
23 ILLUMINA ss1917890595 Feb 12, 2016 (147)
24 ILLUMINA ss1946381119 Feb 12, 2016 (147)
25 ILLUMINA ss1959566646 Feb 12, 2016 (147)
26 HUMAN_LONGEVITY ss2203286712 Dec 20, 2016 (150)
27 TOPMED ss2367671452 Dec 20, 2016 (150)
28 ILLUMINA ss2633171357 Nov 08, 2017 (151)
29 GNOMAD ss2740831439 Nov 08, 2017 (151)
30 GNOMAD ss2749171931 Nov 08, 2017 (151)
31 GNOMAD ss2929495536 Nov 08, 2017 (151)
32 ILLUMINA ss3021583595 Nov 08, 2017 (151)
33 TOPMED ss3215317352 Nov 08, 2017 (151)
34 ILLUMINA ss3627256049 Oct 12, 2018 (152)
35 ILLUMINA ss3634584356 Oct 12, 2018 (152)
36 ILLUMINA ss3638059685 Oct 12, 2018 (152)
37 ILLUMINA ss3640291683 Oct 12, 2018 (152)
38 ILLUMINA ss3643045791 Oct 12, 2018 (152)
39 ILLUMINA ss3644634246 Oct 12, 2018 (152)
40 ILLUMINA ss3651978466 Oct 12, 2018 (152)
41 ILLUMINA ss3725461174 Jul 13, 2019 (153)
42 ILLUMINA ss3744413898 Jul 13, 2019 (153)
43 ILLUMINA ss3744884973 Jul 13, 2019 (153)
44 EVA ss3752516906 Jul 13, 2019 (153)
45 ILLUMINA ss3772383750 Jul 13, 2019 (153)
46 EVA ss3824865748 Apr 27, 2020 (154)
47 SGDP_PRJ ss3881837279 Apr 27, 2020 (154)
48 EVA ss4017678629 Apr 27, 2021 (155)
49 TOPMED ss4976108612 Apr 27, 2021 (155)
50 1000Genomes NC_000014.8 - 74823643 Oct 12, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 74823643 Oct 12, 2018 (152)
52 ExAC NC_000014.8 - 74823643 Oct 12, 2018 (152)
53 gnomAD - Genomes NC_000014.9 - 74356940 Apr 27, 2021 (155)
54 gnomAD - Exomes NC_000014.8 - 74823643 Jul 13, 2019 (153)
55 GO Exome Sequencing Project NC_000014.8 - 74823643 Oct 12, 2018 (152)
56 HapMap NC_000014.9 - 74356940 Apr 27, 2020 (154)
57 SGDP_PRJ NC_000014.8 - 74823643 Apr 27, 2020 (154)
58 TopMed NC_000014.9 - 74356940 Apr 27, 2021 (155)
59 UK 10K study - Twins NC_000014.8 - 74823643 Oct 12, 2018 (152)
60 ALFA NC_000014.9 - 74356940 Apr 27, 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
ss169936670, ss211539163, ss491690375, ss3643045791 NC_000014.7:73893395:C:T NC_000014.9:74356939:C:T (self)
64638966, 35919628, 1907825, 10086922, 1323073, 33854259, 35919628, ss342391774, ss463899356, ss491072435, ss491487299, ss537057968, ss564187723, ss780703052, ss783377412, ss1067547127, ss1351634028, ss1632076168, ss1675070201, ss1691556464, ss1752141929, ss1917890595, ss1946381119, ss1959566646, ss2367671452, ss2633171357, ss2740831439, ss2749171931, ss2929495536, ss3021583595, ss3627256049, ss3634584356, ss3638059685, ss3640291683, ss3644634246, ss3651978466, ss3744413898, ss3744884973, ss3752516906, ss3772383750, ss3824865748, ss3881837279, ss4017678629 NC_000014.8:74823642:C:T NC_000014.9:74356939:C:T (self)
455755207, 1176062, 119933985, 191654271, 9400172541, ss2203286712, ss3215317352, ss3725461174, ss4976108612 NC_000014.9:74356939:C:T NC_000014.9:74356939:C:T (self)
ss3179289, ss69162116, ss74855126, ss159729625, ss173195650 NT_026437.12:55823642:C:T NC_000014.9:74356939:C:T (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 rs2232032

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