11-104891260-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000375726.6(CASP12):c.577G>A(p.Asp193Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00257 in 1,536,382 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 (★).
Frequency
Consequence
ENST00000375726.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASP12 | NR_034068.4 | n.227-737G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASP12 | ENST00000613512.4 | c.577G>A | p.Asp193Asn | missense_variant | 4/8 | 1 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.00916 AC: 1390AN: 151828Hom.: 17 Cov.: 32
GnomAD3 exomes AF: 0.00443 AC: 633AN: 142780Hom.: 8 AF XY: 0.00487 AC XY: 373AN XY: 76640
GnomAD4 exome AF: 0.00185 AC: 2558AN: 1384436Hom.: 50 Cov.: 32 AF XY: 0.00221 AC XY: 1507AN XY: 683188
GnomAD4 genome ? AF: 0.00918 AC: 1395AN: 151946Hom.: 17 Cov.: 32 AF XY: 0.00916 AC XY: 680AN XY: 74268
ClinVar
Submissions by phenotype
CASP12-related disorder Benign:1
Benign, criteria provided, single submitter | 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