rs144985256
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000218.3(KCNQ1):c.1332G>A(p.Thr444=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,613,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T444T) has been classified as Likely benign.
Frequency
Consequence
NM_000218.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.1332G>A | p.Thr444= | synonymous_variant | 10/16 | ENST00000155840.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.1332G>A | p.Thr444= | synonymous_variant | 10/16 | 1 | NM_000218.3 | P1 | |
KCNQ1 | ENST00000335475.6 | c.951G>A | p.Thr317= | synonymous_variant | 10/16 | 1 | |||
KCNQ1 | ENST00000496887.7 | c.975G>A | p.Thr325= | synonymous_variant | 10/16 | 5 | |||
KCNQ1 | ENST00000646564.2 | c.792G>A | p.Thr264= | synonymous_variant | 5/11 |
Frequencies
GnomAD3 genomes AF: 0.000454 AC: 69AN: 151966Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000156 AC: 39AN: 250550Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135520
GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461226Hom.: 0 Cov.: 32 AF XY: 0.0000647 AC XY: 47AN XY: 726890
GnomAD4 genome AF: 0.000460 AC: 70AN: 152084Hom.: 0 Cov.: 33 AF XY: 0.000417 AC XY: 31AN XY: 74352
ClinVar
Submissions by phenotype
Long QT syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Feb 05, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 19, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Beckwith-Wiedemann syndrome;C1837014:Atrial fibrillation, familial, 3;C1865019:Short QT syndrome type 2;C4551509:Jervell and Lange-Nielsen syndrome 1;C4551647:Long QT syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 21, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 18, 2020 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 2016 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Cardiac arrhythmia Benign:1
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Sep 30, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at