rs376180501
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_000238.4(KCNH2):c.3348G>T(p.Ala1116=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000711 in 1,407,182 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. A1116A) has been classified as Likely benign.
Frequency
Consequence
NM_000238.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH2 | NM_000238.4 | c.3348G>T | p.Ala1116= | synonymous_variant | 15/15 | ENST00000262186.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH2 | ENST00000262186.10 | c.3348G>T | p.Ala1116= | synonymous_variant | 15/15 | 1 | NM_000238.4 | P1 | |
KCNH2 | ENST00000330883.9 | c.2328G>T | p.Ala776= | synonymous_variant | 11/11 | 1 | |||
KCNH2 | ENST00000684241.1 | n.4181G>T | non_coding_transcript_exon_variant | 13/13 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000612 AC: 1AN: 163508Hom.: 0 AF XY: 0.0000115 AC XY: 1AN XY: 87012
GnomAD4 exome AF: 7.11e-7 AC: 1AN: 1407182Hom.: 0 Cov.: 31 AF XY: 0.00000144 AC XY: 1AN XY: 694780
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 09, 2023 | - - |
Cardiac arrhythmia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Nov 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at