11-105029866-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001257118.3(CASP1):c.661C>T(p.Arg221Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000479 in 1,613,652 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001257118.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASP1 | NM_001257118.3 | c.661C>T | p.Arg221Cys | missense_variant | 6/9 | ENST00000533400.6 | |
LOC124902742 | XR_007062869.1 | n.41-1481G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASP1 | ENST00000533400.6 | c.661C>T | p.Arg221Cys | missense_variant | 6/9 | 1 | NM_001257118.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000509 AC: 128AN: 251258Hom.: 0 AF XY: 0.000619 AC XY: 84AN XY: 135798
GnomAD4 exome AF: 0.000507 AC: 741AN: 1461440Hom.: 1 Cov.: 33 AF XY: 0.000542 AC XY: 394AN XY: 727050
GnomAD4 genome AF: 0.000210 AC: 32AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74420
ClinVar
Submissions by phenotype
CASP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 19, 2023 | This variant is classified as likely 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