11-1608022-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001012708.2(KRTAP5-3):c.364G>A(p.Gly122Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000986 in 1,613,100 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_001012708.2 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: 0.0000725 AC: 11AN: 151828Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250804Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135694
GnomAD4 exome AF: 0.000101 AC: 148AN: 1461272Hom.: 0 Cov.: 136 AF XY: 0.000111 AC XY: 81AN XY: 726920
GnomAD4 genome AF: 0.0000725 AC: 11AN: 151828Hom.: 0 Cov.: 30 AF XY: 0.0000809 AC XY: 6AN XY: 74152
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.364G>A (p.G122S) alteration is located in exon 1 (coding exon 1) of the KRTAP5-3 gene. This alteration results from a G to A substitution at nucleotide position 364, causing the glycine (G) at amino acid position 122 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