chr4-184632273-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004346.4(CASP3):c.302G>A(p.Arg101His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000182 in 1,611,346 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 Likely benign (★).
Frequency
Consequence
NM_004346.4 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 |
---|---|---|---|---|---|---|---|
CASP3 | NM_004346.4 | c.302G>A | p.Arg101His | missense_variant | 5/8 | ENST00000308394.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASP3 | ENST00000308394.9 | c.302G>A | p.Arg101His | missense_variant | 5/8 | 1 | NM_004346.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000966 AC: 147AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000220 AC: 55AN: 250354Hom.: 0 AF XY: 0.000163 AC XY: 22AN XY: 135326
GnomAD4 exome AF: 0.000101 AC: 147AN: 1459130Hom.: 0 Cov.: 30 AF XY: 0.0000964 AC XY: 70AN XY: 725880
GnomAD4 genome ? AF: 0.000966 AC: 147AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000954 AC XY: 71AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at