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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.

rs370244148

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:112514896 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000019 (5/264690, TOPMED)
T=0.000014 (2/140262, GnomAD)
T=0.00005 (1/20446, ALFA) (+ 1 more)
T=0.00008 (1/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
WNT2B : Stop Gained
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.112514896C>A
GRCh38.p13 chr 1 NC_000001.11:g.112514896C>T
GRCh37.p13 chr 1 NC_000001.10:g.113057518C>A
GRCh37.p13 chr 1 NC_000001.10:g.113057518C>T
WNT2B RefSeqGene NG_052953.1:g.53356C>A
WNT2B RefSeqGene NG_052953.1:g.53356C>T
Gene: WNT2B, Wnt family member 2B (plus strand)
Molecule type Change Amino acid[Codon] SO Term
WNT2B transcript variant 3 NM_001291880.1:c.-72= N/A 5 Prime UTR Variant
WNT2B transcript variant WNT-2B1 NM_004185.4:c.148C>A R [CGA] > R [AGA] Coding Sequence Variant
protein Wnt-2b isoform WNT-2B1 NP_004176.2:p.Arg50= R (Arg) > R (Arg) Synonymous Variant
WNT2B transcript variant WNT-2B1 NM_004185.4:c.148C>T R [CGA] > * [TGA] Coding Sequence Variant
protein Wnt-2b isoform WNT-2B1 NP_004176.2:p.Arg50Ter R (Arg) > * (Ter) Stop Gained
WNT2B transcript variant WNT-2B2 NM_024494.3:c.205C>A R [CGA] > R [AGA] Coding Sequence Variant
protein Wnt-2b isoform WNT-2B2 NP_078613.1:p.Arg69= R (Arg) > R (Arg) Synonymous Variant
WNT2B transcript variant WNT-2B2 NM_024494.3:c.205C>T R [CGA] > * [TGA] Coding Sequence Variant
protein Wnt-2b isoform WNT-2B2 NP_078613.1:p.Arg69Ter R (Arg) > * (Ter) Stop Gained
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.

Allele: T (allele ID: 535693 )
ClinVar Accession Disease Names Clinical Significance
RCV000656393.1 Chronic diarrhea,Diarrhea,Failure to thrive,Failure to thrive in infancy,Impaired feeding ability Pathogenic
RCV000714963.1 Diarrhea 9 Pathogenic

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 20446 C=0.99995 T=0.00005
European Sub 15838 C=1.00000 T=0.00000
African Sub 2898 C=0.9997 T=0.0003
African Others Sub 114 C=1.000 T=0.000
African American Sub 2784 C=0.9996 T=0.0004
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 744 C=1.000 T=0.000


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=0.999981 T=0.000019
gnomAD - Genomes Global Study-wide 140262 C=0.999986 T=0.000014
gnomAD - Genomes European Sub 75936 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 42052 C=0.99995 T=0.00005
gnomAD - Genomes American Sub 13664 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 20446 C=0.99995 T=0.00005
Allele Frequency Aggregator European Sub 15838 C=1.00000 T=0.00000
Allele Frequency Aggregator African Sub 2898 C=0.9997 T=0.0003
Allele Frequency Aggregator Other Sub 744 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9998 T=0.0002
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= A T
GRCh38.p13 chr 1 NC_000001.11:g.112514896= NC_000001.11:g.112514896C>A NC_000001.11:g.112514896C>T
GRCh37.p13 chr 1 NC_000001.10:g.113057518= NC_000001.10:g.113057518C>A NC_000001.10:g.113057518C>T
WNT2B RefSeqGene NG_052953.1:g.53356= NG_052953.1:g.53356C>A NG_052953.1:g.53356C>T
WNT2B transcript variant WNT-2B1 NM_004185.4:c.148= NM_004185.4:c.148C>A NM_004185.4:c.148C>T
WNT2B transcript variant WNT-2B1 NM_004185.3:c.148= NM_004185.3:c.148C>A NM_004185.3:c.148C>T
WNT2B transcript variant 3 NM_001291880.1:c.-72= NM_001291880.1:c.-72C>A NM_001291880.1:c.-72C>T
WNT2B transcript variant WNT-2B2 NM_024494.3:c.205= NM_024494.3:c.205C>A NM_024494.3:c.205C>T
WNT2B transcript variant WNT-2B2 NM_024494.2:c.205= NM_024494.2:c.205C>A NM_024494.2:c.205C>T
protein Wnt-2b isoform WNT-2B1 NP_004176.2:p.Arg50= NP_004176.2:p.Arg50= NP_004176.2:p.Arg50Ter
protein Wnt-2b isoform WNT-2B2 NP_078613.1:p.Arg69= NP_078613.1:p.Arg69= NP_078613.1:p.Arg69Ter
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#.

10 SubSNP, 8 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712332557 Apr 25, 2013 (138)
2 EVA_EXAC ss1685691671 Apr 01, 2015 (144)
3 EVA_EXAC ss1685691672 Apr 01, 2015 (144)
4 GNOMAD ss2731720432 Nov 08, 2017 (151)
5 AFFY ss2984871204 Nov 08, 2017 (151)
6 TOPMED ss3087035393 Nov 08, 2017 (151)
7 ILLUMINA ss3653643250 Oct 11, 2018 (152)
8 EVA ss3823642306 Apr 25, 2020 (154)
9 GNOMAD ss4000590392 Apr 25, 2021 (155)
10 TOPMED ss4463919008 Apr 25, 2021 (155)
11 ExAC

Submission ignored due to conflicting rows:
Row 4900962 (NC_000001.10:113057517:C:C 121373/121376, NC_000001.10:113057517:C:A 3/121376)
Row 4900963 (NC_000001.10:113057517:C:C 121375/121376, NC_000001.10:113057517:C:T 1/121376)

- Oct 11, 2018 (152)
12 ExAC

Submission ignored due to conflicting rows:
Row 4900962 (NC_000001.10:113057517:C:C 121373/121376, NC_000001.10:113057517:C:A 3/121376)
Row 4900963 (NC_000001.10:113057517:C:C 121375/121376, NC_000001.10:113057517:C:T 1/121376)

- Oct 11, 2018 (152)
13 gnomAD - Genomes NC_000001.11 - 112514896 Apr 25, 2021 (155)
14 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 744144 (NC_000001.10:113057517:C:C 251464/251468, NC_000001.10:113057517:C:A 4/251468)
Row 744145 (NC_000001.10:113057517:C:C 251465/251468, NC_000001.10:113057517:C:T 3/251468)

- Jul 12, 2019 (153)
15 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 744144 (NC_000001.10:113057517:C:C 251464/251468, NC_000001.10:113057517:C:A 4/251468)
Row 744145 (NC_000001.10:113057517:C:C 251465/251468, NC_000001.10:113057517:C:T 3/251468)

- Jul 12, 2019 (153)
16 GO Exome Sequencing Project NC_000001.10 - 113057518 Oct 11, 2018 (152)
17 TopMed NC_000001.11 - 112514896 Apr 25, 2021 (155)
18 ALFA NC_000001.11 - 112514896 Apr 25, 2021 (155)
19 ClinVar RCV000656393.1 Oct 11, 2018 (152)
20 ClinVar RCV000714963.1 Jul 12, 2019 (153)
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
ss1685691672, ss2731720432 NC_000001.10:113057517:C:A NC_000001.11:112514895:C:A (self)
100938, ss712332557, ss1685691671, ss2731720432, ss2984871204, ss3653643250, ss3823642306 NC_000001.10:113057517:C:T NC_000001.11:112514895:C:T (self)
RCV000656393.1, RCV000714963.1, 22945616, 17340095, 27525343, 560237606, ss3087035393, ss4000590392, ss4463919008 NC_000001.11:112514895:C:T NC_000001.11:112514895: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 rs370244148

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