17-41184442-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001386841.1(KRTAP4-1):c.413G>A(p.Arg138His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,603,788 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R138C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001386841.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRTAP4-1 | NM_001386841.1 | c.413G>A | p.Arg138His | missense_variant | Exon 1 of 1 | ENST00000398472.2 | NP_001373770.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00586 AC: 892AN: 152188Hom.: 13 Cov.: 34
GnomAD3 exomes AF: 0.00141 AC: 346AN: 244672Hom.: 2 AF XY: 0.00113 AC XY: 149AN XY: 132342
GnomAD4 exome AF: 0.000573 AC: 832AN: 1451482Hom.: 7 Cov.: 77 AF XY: 0.000473 AC XY: 341AN XY: 720248
GnomAD4 genome AF: 0.00590 AC: 898AN: 152306Hom.: 13 Cov.: 34 AF XY: 0.00572 AC XY: 426AN XY: 74482
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at