17-41047126-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001123387.1(KRTAP2-1):c.142C>T(p.Pro48Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000727 in 151,346 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001123387.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP2-1 | NM_001123387.1 | c.142C>T | p.Pro48Ser | missense_variant | 1/1 | ENST00000391419.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP2-1 | ENST00000391419.3 | c.142C>T | p.Pro48Ser | missense_variant | 1/1 | NM_001123387.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000727 AC: 11AN: 151228Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000811 AC: 5AN: 61642Hom.: 0 AF XY: 0.0000322 AC XY: 1AN XY: 31040
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000609 AC: 73AN: 1199476Hom.: 0 Cov.: 23 AF XY: 0.0000580 AC XY: 34AN XY: 586254
GnomAD4 genome AF: 0.0000727 AC: 11AN: 151346Hom.: 0 Cov.: 31 AF XY: 0.0000676 AC XY: 5AN XY: 73936
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at