6-39190997-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003740.4(KCNK5):c.1393C>A(p.Pro465Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00313 in 1,576,484 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003740.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNK5 | NM_003740.4 | c.1393C>A | p.Pro465Thr | missense_variant | 5/5 | ENST00000359534.4 | |
KCNK5 | XM_005249456.2 | c.1384C>A | p.Pro462Thr | missense_variant | 5/5 | ||
KCNK5 | XM_006715235.2 | c.847C>A | p.Pro283Thr | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNK5 | ENST00000359534.4 | c.1393C>A | p.Pro465Thr | missense_variant | 5/5 | 1 | NM_003740.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0170 AC: 2584AN: 152198Hom.: 70 Cov.: 32
GnomAD3 exomes AF: 0.00437 AC: 900AN: 206138Hom.: 18 AF XY: 0.00281 AC XY: 312AN XY: 111080
GnomAD4 exome AF: 0.00165 AC: 2345AN: 1424168Hom.: 69 Cov.: 32 AF XY: 0.00142 AC XY: 1005AN XY: 705432
GnomAD4 genome AF: 0.0170 AC: 2583AN: 152316Hom.: 70 Cov.: 32 AF XY: 0.0162 AC XY: 1210AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 29, 2020 | This variant is associated with the following publications: (PMID: 26220970) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at