6-39191396-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_003740.4(KCNK5):c.994G>A(p.Gly332Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 1,613,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003740.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNK5 | NM_003740.4 | c.994G>A | p.Gly332Ser | missense_variant | Exon 5 of 5 | ENST00000359534.4 | NP_003731.1 | |
KCNK5 | XM_005249456.2 | c.985G>A | p.Gly329Ser | missense_variant | Exon 5 of 5 | XP_005249513.1 | ||
KCNK5 | XM_006715235.2 | c.448G>A | p.Gly150Ser | missense_variant | Exon 3 of 3 | XP_006715298.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000467 AC: 71AN: 152114Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000172 AC: 43AN: 250428Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135512
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1461104Hom.: 0 Cov.: 32 AF XY: 0.0000495 AC XY: 36AN XY: 726890
GnomAD4 genome AF: 0.000473 AC: 72AN: 152232Hom.: 0 Cov.: 31 AF XY: 0.000484 AC XY: 36AN XY: 74418
ClinVar
Submissions by phenotype
KCNK5-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at