11-1585096-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001005922.1(KRTAP5-1):c.154G>A(p.Val52Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000771 in 1,542,508 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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. V52G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005922.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP5-1 | NM_001005922.1 | c.154G>A | p.Val52Met | missense_variant | 1/1 | ENST00000382171.2 | |
KRTAP5-AS1 | NR_021489.2 | n.328+12028C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP5-1 | ENST00000382171.2 | c.154G>A | p.Val52Met | missense_variant | 1/1 | NM_001005922.1 | P1 | ||
KRTAP5-AS1 | ENST00000424148.1 | n.328+12028C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000175 AC: 22AN: 126032Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.000132 AC: 32AN: 241878Hom.: 0 AF XY: 0.000145 AC XY: 19AN XY: 131036
GnomAD4 exome AF: 0.0000678 AC: 96AN: 1416372Hom.: 4 Cov.: 39 AF XY: 0.0000979 AC XY: 69AN XY: 704780
GnomAD4 genome AF: 0.000182 AC: 23AN: 126136Hom.: 0 Cov.: 26 AF XY: 0.000179 AC XY: 11AN XY: 61312
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at