6-39194301-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003740.4(KCNK5):c.502G>A(p.Val168Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000151 in 1,613,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003740.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNK5 | NM_003740.4 | c.502G>A | p.Val168Met | missense_variant | 4/5 | ENST00000359534.4 | |
KCNK5 | XM_005249456.2 | c.493G>A | p.Val165Met | missense_variant | 4/5 | ||
KCNK5 | XM_006715235.2 | c.-45G>A | 5_prime_UTR_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNK5 | ENST00000359534.4 | c.502G>A | p.Val168Met | missense_variant | 4/5 | 1 | NM_003740.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250322Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135262
GnomAD4 exome AF: 0.000142 AC: 207AN: 1461088Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 98AN XY: 726830
GnomAD4 genome AF: 0.000243 AC: 37AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.502G>A (p.V168M) alteration is located in exon 4 (coding exon 4) of the KCNK5 gene. This alteration results from a G to A substitution at nucleotide position 502, causing the valine (V) at amino acid position 168 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at