14-62981048-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_139318.5(KCNH5):c.766G>A(p.Val256Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000821 in 1,461,854 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 Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V256L) has been classified as Uncertain significance.
Frequency
Consequence
NM_139318.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH5 | NM_139318.5 | c.766G>A | p.Val256Ile | missense_variant | 6/11 | ENST00000322893.12 | |
KCNH5 | NM_172375.3 | c.766G>A | p.Val256Ile | missense_variant | 6/10 | ||
KCNH5 | XM_047431275.1 | c.766G>A | p.Val256Ile | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH5 | ENST00000322893.12 | c.766G>A | p.Val256Ile | missense_variant | 6/11 | 1 | NM_139318.5 | P1 | |
KCNH5 | ENST00000420622.6 | c.766G>A | p.Val256Ile | missense_variant | 6/10 | 1 | |||
KCNH5 | ENST00000394964.3 | n.931G>A | non_coding_transcript_exon_variant | 6/7 | 1 | ||||
KCNH5 | ENST00000394968.2 | c.592G>A | p.Val198Ile | missense_variant | 6/11 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251316Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135828
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461854Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727222
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at