14-62707586-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_139318.5(KCNH5):c.2889C>T(p.Pro963=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000718 in 1,531,356 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. P963P) has been classified as Likely benign.
Frequency
Consequence
NM_139318.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNH5 | NM_139318.5 | c.2889C>T | p.Pro963= | synonymous_variant | 11/11 | ENST00000322893.12 | |
KCNH5 | NM_172375.3 | c.*856C>T | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNH5 | ENST00000322893.12 | c.2889C>T | p.Pro963= | synonymous_variant | 11/11 | 1 | NM_139318.5 | P1 | |
KCNH5 | ENST00000420622.6 | c.*856C>T | 3_prime_UTR_variant | 10/10 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000102 AC: 2AN: 195148Hom.: 0 AF XY: 0.0000194 AC XY: 2AN XY: 102892
GnomAD4 exome AF: 0.00000652 AC: 9AN: 1379324Hom.: 0 Cov.: 29 AF XY: 0.00000444 AC XY: 3AN XY: 675498
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152032Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at