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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 151

Released July 17, 2018

Homo sapiens
chr1:115683980 (GRCh38.p7) 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
C=0.00001 (3/246230, GnomAD)
C=0.00004 (5/125568, TOPMED)
C=0.00002 (2/121248, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
VANGL1 : Missense Variant
1 citation
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.p7 chr 1 NC_000001.11:g.115683980T>C
GRCh37.p13 chr 1 NC_000001.10:g.116226601T>C
VANGL1 RefSeqGene NG_016548.1:g.47028T>C
Gene: VANGL1, VANGL planar cell polarity protein 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
VANGL1 transcript variant 1 NM_138959.2:c.983T>C M [ATG] > T [ACG] Coding Sequence Variant
vang-like protein 1 isoform 1 NP_620409.1:p.Met...


M (Met) > T (Thr) Missense Variant
VANGL1 transcript variant 3 NM_001172411.1:c....


M [ATG] > T [ACG] Coding Sequence Variant
vang-like protein 1 isoform 2 NP_001165882.1:p....


M (Met) > T (Thr) Missense Variant
VANGL1 transcript variant 2 NM_001172412.1:c....


M [ATG] > T [ACG] Coding Sequence Variant
vang-like protein 1 isoform 1 NP_001165883.1:p....


M (Met) > T (Thr) Missense 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.

Allele: C (allele ID: 16387 )
ClinVar Accession Disease Names Clinical Significance
RCV000001413.4 Neural tube defects, susceptibility to Risk-Factor

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
The Genome Aggregation Database Global Study-wide 246230 T=0.99999 C=0.00001
The Genome Aggregation Database European Sub 133982 T=0.99999 C=0.00001
The Genome Aggregation Database Asian Sub 48030 T=1.0000 C=0.0000
The Genome Aggregation Database American Sub 33582 T=1.0000 C=0.0000
The Genome Aggregation Database African Sub 15300 T=1.0000 C=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 T=1.000 C=0.000
The Genome Aggregation Database Other Sub 5486 T=1.000 C=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.99996 C=0.00004
The Exome Aggregation Consortium Global Study-wide 121248 T=0.99998 C=0.00002
The Exome Aggregation Consortium Europe Sub 73222 T=1.0000 C=0.0000
The Exome Aggregation Consortium Asian Sub 25160 T=1.0000 C=0.0000
The Exome Aggregation Consortium American Sub 11572 T=1.0000 C=0.0000
The Exome Aggregation Consortium African Sub 10386 T=1.0000 C=0.0000
The Exome Aggregation Consortium Other Sub 908 T=1.00 C=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 T= C Note
GRCh38.p7 chr 1 NC_000001.11:g.115683980T= NC_000001.11:g.11568398...


GRCh37.p13 chr 1 NC_000001.10:g.116226601T= NC_000001.10:g.11622660...


VANGL1 RefSeqGene NG_016548.1:g.47028T= NG_016548.1:g.47028T>C
VANGL1 transcript variant 1 NM_138959.2:c.983T= NM_138959.2:c.983T>C
VANGL1 transcript variant 3 NM_001172411.1:c.977T= NM_001172411.1:c.977T>C
VANGL1 transcript variant 2 NM_001172412.1:c.983T= NM_001172412.1:c.983T>C
vang-like protein 1 isoform 1 NP_620409.1:p.Met328= NP_620409.1:p.Met328Thr
vang-like protein 1 isoform 2 NP_001165882.1:p.Met326= NP_001165882.1:p.Met326Thr
vang-like protein 1 isoform 1 NP_001165883.1:p.Met328= NP_001165883.1:p.Met328Thr

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#.

3 Frequency, 8 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss275517701 Dec 03, 2010 (133)
2 NHLBI-ESP ss712335163 Apr 25, 2013 (138)
3 EVA_EXAC ss1685705604 Apr 01, 2015 (144)
4 ILLUMINA ss1958305834 Feb 12, 2016 (147)
5 TOPMED ss2328332330 Dec 20, 2016 (150)
6 GNOMAD ss2731741599 Nov 08, 2017 (151)
7 ILLUMINA ss3021124057 Nov 08, 2017 (151)
8 TOPMED ss3087600541 Nov 08, 2017 (151)
9 The Exome Aggregation Consortium NC_000001.10 - 116226601 Jul 19, 2018 (151)
10 The Genome Aggregation Database NC_000001.10 - 116226601 Jul 19, 2018 (151)
11 Trans-Omics for Precision Medicine NC_000001.11 - 115683980 Jul 19, 2018 (151)
12 ClinVar RCV000001413.4 Jul 19, 2018 (151)

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
4916203, 756334, ss712335163, ss1685705604, ss1958305834, ss2328332330, ss2731741599, ss3021124057 NC_000001.10:116226600:T= NC_000001.11:115683979:T= (self)
17820236, ss275517701, ss3087600541 NC_000001.11:115683979:T= NC_000001.11:115683979:T= (self)
4916203, 756334, ss712335163, ss1685705604, ss1958305834, ss2328332330, ss2731741599, ss3021124057 NC_000001.10:116226600:T>C NC_000001.11:115683979:T>C (self)
RCV000001413.4, 17820236, ss275517701, ss3087600541 NC_000001.11:115683979:T>C NC_000001.11:115683979:T>C (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs121918220
PMID Title Author Year Journal
17409324 Mutations in VANGL1 associated with neural-tube defects. Kibar Z et al. 2007 The New England journal of medicine

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: 0.1.4.post833+d3ba21e