chr14-62707585-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_ModerateBP6_Moderate
The NM_139318.5(KCNH5):c.2890C>A(p.Gln964Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000218 in 1,375,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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. Q964E) has been classified as Uncertain significance.
Frequency
Consequence
NM_139318.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH5 | NM_139318.5 | c.2890C>A | p.Gln964Lys | missense_variant | 11/11 | ENST00000322893.12 | |
KCNH5 | NM_172375.3 | c.*857C>A | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH5 | ENST00000322893.12 | c.2890C>A | p.Gln964Lys | missense_variant | 11/11 | 1 | NM_139318.5 | P1 | |
KCNH5 | ENST00000420622.6 | c.*857C>A | 3_prime_UTR_variant | 10/10 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000103 AC: 2AN: 194438Hom.: 0 AF XY: 0.0000195 AC XY: 2AN XY: 102522
GnomAD4 exome AF: 0.0000218 AC: 30AN: 1375954Hom.: 0 Cov.: 29 AF XY: 0.0000282 AC XY: 19AN XY: 673614
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 | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at