5-35910456-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001042625.2(CAPSL):c.225G>A(p.Met75Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,320 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001042625.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPSL | NM_001042625.2 | c.225G>A | p.Met75Ile | missense_variant | 3/5 | ENST00000651391.1 | NP_001036090.1 | |
CAPSL | NM_144647.4 | c.225G>A | p.Met75Ile | missense_variant | 3/5 | NP_653248.3 | ||
CAPSL | XM_006714444.4 | c.276G>A | p.Met92Ile | missense_variant | 3/5 | XP_006714507.1 | ||
CAPSL | XM_006714445.4 | c.276G>A | p.Met92Ile | missense_variant | 3/5 | XP_006714508.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPSL | ENST00000651391.1 | c.225G>A | p.Met75Ile | missense_variant | 3/5 | NM_001042625.2 | ENSP00000498465.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461320Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727044
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2022 | The c.225G>A (p.M75I) alteration is located in exon 3 (coding exon 2) of the CAPSL gene. This alteration results from a G to A substitution at nucleotide position 225, causing the methionine (M) at amino acid position 75 to be replaced by an isoleucine (I). 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