chr10-113697537-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001227.5(CASP7):c.44A>T(p.Asp15Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001227.5 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 |
---|---|---|---|---|---|---|---|
CASP7 | NM_001227.5 | c.44A>T | p.Asp15Val | missense_variant | 2/7 | ENST00000369318.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASP7 | ENST00000369318.8 | c.44A>T | p.Asp15Val | missense_variant | 2/7 | 1 | NM_001227.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251452Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135900
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461752Hom.: 0 Cov.: 30 AF XY: 0.0000399 AC XY: 29AN XY: 727198
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 20, 2024 | The c.143A>T (p.D48V) alteration is located in exon 3 (coding exon 2) of the CASP7 gene. This alteration results from a A to T substitution at nucleotide position 143, causing the aspartic acid (D) at amino acid position 48 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at