11-104891194-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000375726.6(CASP12):āc.643A>Gā(p.Ile215Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00259 in 1,536,496 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
ENST00000375726.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CASP12 | NR_034068.4 | n.227-671A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASP12 | ENST00000613512.4 | c.643A>G | p.Ile215Val | missense_variant | 4/8 | 1 | ENSP00000482745 | P5 |
Frequencies
GnomAD3 genomes AF: 0.00919 AC: 1397AN: 151974Hom.: 17 Cov.: 32
GnomAD3 exomes AF: 0.00443 AC: 638AN: 144016Hom.: 8 AF XY: 0.00489 AC XY: 377AN XY: 77078
GnomAD4 exome AF: 0.00186 AC: 2571AN: 1384404Hom.: 50 Cov.: 32 AF XY: 0.00221 AC XY: 1513AN XY: 683206
GnomAD4 genome AF: 0.00922 AC: 1402AN: 152092Hom.: 17 Cov.: 32 AF XY: 0.00915 AC XY: 680AN XY: 74352
ClinVar
Submissions by phenotype
CASP12-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at