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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 Aliases 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.

rs587784572

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr12:14641142 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00003 (8/251246, GnomAD_exome)
T=0.00002 (2/125568, TOPMED)
T=0.00003 (4/121362, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GUCY2C : Missense Variant
C12orf60 : Intron Variant
Publications
1 citation
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 12 NC_000012.12:g.14641142C>T
GRCh37.p13 chr 12 NC_000012.11:g.14794076C>T
GUCY2C RefSeqGene NG_052021.1:g.60444G>A
Gene: C12orf60, chromosome 12 open reading frame 60 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
C12orf60 transcript NM_175874.4:c. N/A Genic Upstream Transcript Variant
C12orf60 transcript variant X3 XM_005253322.4:c. N/A Genic Upstream Transcript Variant
C12orf60 transcript variant X5 XM_011520568.2:c. N/A Genic Upstream Transcript Variant
C12orf60 transcript variant X4 XM_011520569.2:c. N/A Genic Upstream Transcript Variant
C12orf60 transcript variant X6 XM_017018873.1:c. N/A Genic Upstream Transcript Variant
C12orf60 transcript variant X7 XM_017018874.1:c. N/A Genic Upstream Transcript Variant
C12orf60 transcript variant X1 XM_024448858.1:c. N/A Genic Upstream Transcript Variant
C12orf60 transcript variant X2 XM_024448859.1:c. N/A Genic Upstream Transcript Variant
C12orf60 transcript variant X8 XR_001748595.1:n. N/A Intron Variant
C12orf60 transcript variant X9 XR_001748596.1:n. N/A Intron Variant
C12orf60 transcript variant X10 XR_001748597.1:n. N/A Intron Variant
C12orf60 transcript variant X12 XR_001748598.2:n. N/A Intron Variant
C12orf60 transcript variant X11 XR_001748599.1:n. N/A Intron Variant
Gene: GUCY2C, guanylate cyclase 2C (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GUCY2C transcript NM_004963.4:c.2008G>A A [GCA] > T [ACA] Coding Sequence Variant
heat-stable enterotoxin receptor precursor NP_004954.2:p.Ala670Thr A (Ala) > T (Thr) Missense Variant
GUCY2C transcript variant X1 XM_011520631.2:c.1762G>A A [GCA] > T [ACA] Coding Sequence Variant
heat-stable enterotoxin receptor isoform X1 XP_011518933.1:p.Ala588Thr A (Ala) > T (Thr) 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.

Allele: T (allele ID: 171003 )
ClinVar Accession Disease Names Clinical Significance
RCV000148339.1 Meconium ileus Pathogenic
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
gnomAD - Exomes Global Study-wide 251246 C=0.99997 T=0.00003
gnomAD - Exomes European Sub 135222 C=0.99998 T=0.00002
gnomAD - Exomes Asian Sub 48986 C=1.0000 T=0.0000
gnomAD - Exomes American Sub 34574 C=0.9999 T=0.0001
gnomAD - Exomes African Sub 16256 C=1.0000 T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6132 C=1.000 T=0.000
TopMed Global Study-wide 125568 C=0.99998 T=0.00002
ExAC Global Study-wide 121362 C=0.99997 T=0.00003
ExAC Europe Sub 73344 C=1.0000 T=0.0000
ExAC Asian Sub 25142 C=1.0000 T=0.0000
ExAC American Sub 11562 C=0.9999 T=0.0001
ExAC African Sub 10406 C=1.0000 T=0.0000
ExAC Other Sub 908 C=1.00 T=0.00
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 Note
GRCh38.p12 chr 12 NC_000012.12:g.14641142= NC_000012.12:g.14641142C>T
GRCh37.p13 chr 12 NC_000012.11:g.14794076= NC_000012.11:g.14794076C>T
GUCY2C RefSeqGene NG_052021.1:g.60444= NG_052021.1:g.60444G>A
GUCY2C transcript NM_004963.4:c.2008= NM_004963.4:c.2008G>A
GUCY2C transcript NM_004963.3:c.2008= NM_004963.3:c.2008G>A
GUCY2C transcript variant X1 XM_011520631.2:c.1762= XM_011520631.2:c.1762G>A
heat-stable enterotoxin receptor precursor NP_004954.2:p.Ala670= NP_004954.2:p.Ala670Thr
heat-stable enterotoxin receptor isoform X1 XP_011518933.1:p.Ala588= XP_011518933.1:p.Ala588Thr
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#.

4 SubSNP, 3 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss1493131973 Dec 05, 2014 (142)
2 EVA_EXAC ss1690807249 Apr 01, 2015 (144)
3 GNOMAD ss2739656268 Nov 08, 2017 (151)
4 TOPMED ss3163635107 Nov 08, 2017 (151)
5 ExAC NC_000012.11 - 14794076 Oct 12, 2018 (152)
6 gnomAD - Exomes NC_000012.11 - 14794076 Jul 13, 2019 (153)
7 TopMed NC_000012.12 - 14641142 Oct 12, 2018 (152)
8 ClinVar RCV000148339.1 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1096100, 8883828, ss1690807249, ss2739656268 NC_000012.11:14794075:C:T NC_000012.12:14641141:C:T (self)
RCV000148339.1, 78374611, ss1493131973, ss3163635107 NC_000012.12:14641141:C:T NC_000012.12:14641141: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.

1 citation for rs587784572
PMID Title Author Year Journal
25370039 Meconium ileus in a Lebanese family secondary to mutations in the GUCY2C gene. Smith A et al. 2015 European journal of human genetics

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.post308+0fe9b3b