chr11-104997445-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004347.5(CASP5):c.1144G>C(p.Glu382Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000959 in 1,613,326 control chromosomes in the GnomAD database, including 3 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 Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004347.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASP5 | NM_004347.5 | c.1144G>C | p.Glu382Gln | missense_variant | 8/10 | ENST00000260315.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASP5 | ENST00000260315.8 | c.1144G>C | p.Glu382Gln | missense_variant | 8/10 | 5 | NM_004347.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000677 AC: 103AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000768 AC: 193AN: 251254Hom.: 0 AF XY: 0.000862 AC XY: 117AN XY: 135780
GnomAD4 exome AF: 0.000988 AC: 1443AN: 1461034Hom.: 3 Cov.: 29 AF XY: 0.000988 AC XY: 718AN XY: 726858
GnomAD4 genome ? AF: 0.000683 AC: 104AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at