17-41307905-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001146182.2(KRTAP16-1):c.1349G>A(p.Arg450His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,550,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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. R450C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001146182.2 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: 0.0000855 AC: 13AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000161 AC: 24AN: 148704Hom.: 0 AF XY: 0.000138 AC XY: 11AN XY: 79970
GnomAD4 exome AF: 0.000124 AC: 173AN: 1398344Hom.: 0 Cov.: 38 AF XY: 0.000130 AC XY: 90AN XY: 689678
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74410
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1349G>A (p.R450H) alteration is located in exon 1 (coding exon 1) of the KRTAP16-1 gene. This alteration results from a G to A substitution at nucleotide position 1349, causing the arginine (R) at amino acid position 450 to be replaced by a histidine (H). 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