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NM_181798.1(KCNQ1):c.747+5G>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 29, 2021)
Last evaluated:
Apr 12, 2021
Accession:
VCV000200842.9
Variation ID:
200842
Description:
single nucleotide variant
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NM_181798.1(KCNQ1):c.747+5G>A

Allele ID
197475
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.5
Genomic location
11: 2585312 (GRCh38) GRCh38 UCSC
11: 2606542 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_287t1:c.1128+5G>A
LRG_287:g.145322G>A
LRG_287t2:c.747+5G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:2585311:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00015
Links
ClinGen: CA005367
dbSNP: rs76735093
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Mar 24, 2021 RCV000182177.5
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000764973.1
Likely benign 1 criteria provided, single submitter Nov 1, 2020 RCV001087240.2
Uncertain significance 1 criteria provided, single submitter Oct 9, 2019 RCV001184234.1
Uncertain significance 1 criteria provided, single submitter Apr 12, 2021 RCV001375390.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNQ1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
1161 1427

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 24, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000234480.11
Submitted: (Sep 29, 2021)
Evidence details
Comment:
In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, … (more)
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Beckwith-Wiedemann syndrome
Long QT syndrome 1
Long QT syndrome 1
Jervell and Lange-Nielsen syndrome 1
Atrial fibrillation, familial, 3
Short QT syndrome 2
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000896150.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Oct 09, 2019)
criteria provided, single submitter
Method: clinical testing
Arrhythmia
Allele origin: germline
Color Health, Inc
Accession: SCV001350175.1
Submitted: (May 19, 2020)
Comment:
This variant causes a G>A nucleotide substitution at the +5 position of intron 8 of the KCNQ1 gene. Splice site prediction tools predict that this … (more)
Evidence details
Likely benign
(Nov 01, 2020)
criteria provided, single submitter
Method: clinical testing
Long QT syndrome
Allele origin: germline
Invitae
Accession: SCV001004227.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Apr 12, 2021)
criteria provided, single submitter
Method: clinical testing
Hearing impairment
Allele origin: germline
Department of Otolaryngology – Head & Neck Surgery,Cochlear Implant Center
Accession: SCV001571823.2
Submitted: (Aug 17, 2021)
Evidence details
Publications
PubMed (3)
Comment:
PM2_Supporting, BP4_Supporting

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Green RC Genetics in medicine : official journal of the American College of Medical Genetics 2013 PMID: 23788249
Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Kapplinger JD Heart rhythm 2009 PMID: 19716085

Text-mined citations for rs76735093...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021