NM_031962.3:c.65C>G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031962.3(KRTAP9-3):c.65C>G(p.Thr22Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000811 in 1,603,380 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031962.3 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: 0.00000674 AC: 1AN: 148348Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250392Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135444
GnomAD4 exome AF: 0.00000825 AC: 12AN: 1455032Hom.: 1 Cov.: 37 AF XY: 0.0000124 AC XY: 9AN XY: 724122
GnomAD4 genome AF: 0.00000674 AC: 1AN: 148348Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 1AN XY: 72502
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.65C>G (p.T22S) alteration is located in exon 1 (coding exon 1) of the KRTAP9-3 gene. This alteration results from a C to G substitution at nucleotide position 65, causing the threonine (T) at amino acid position 22 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