chr20-44750605-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022358.4(KCNK15):c.760C>T(p.Pro254Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000998 in 1,603,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P254L) has been classified as Uncertain significance.
Frequency
Consequence
NM_022358.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151946Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000172 AC: 4AN: 233142Hom.: 0 AF XY: 0.0000235 AC XY: 3AN XY: 127716
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1451408Hom.: 0 Cov.: 39 AF XY: 0.0000125 AC XY: 9AN XY: 722406
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151946Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74206
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.760C>T (p.P254S) alteration is located in exon 2 (coding exon 2) of the KCNK15 gene. This alteration results from a C to T substitution at nucleotide position 760, causing the proline (P) at amino acid position 254 to be replaced by a serine (S). 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