2-27443089-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173853.4(KRTCAP3):c.289G>A(p.Ala97Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,668 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_173853.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTCAP3 | NM_173853.4 | c.289G>A | p.Ala97Thr | missense_variant | 4/7 | ENST00000288873.7 | |
KRTCAP3 | NM_001168364.2 | c.289G>A | p.Ala97Thr | missense_variant | 4/7 | ||
KRTCAP3 | NM_001321325.2 | c.289G>A | p.Ala97Thr | missense_variant | 4/7 | ||
KRTCAP3 | XM_047443704.1 | c.289G>A | p.Ala97Thr | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTCAP3 | ENST00000288873.7 | c.289G>A | p.Ala97Thr | missense_variant | 4/7 | 1 | NM_173853.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250872Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135770
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461570Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727086
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2022 | The c.289G>A (p.A97T) alteration is located in exon 4 (coding exon 4) of the KRTCAP3 gene. This alteration results from a G to A substitution at nucleotide position 289, causing the alanine (A) at amino acid position 97 to be replaced by a threonine (T). 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