12-75282301-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001355024.4(CAPS2):c.1448T>C(p.Ile483Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00026 in 1,608,538 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_001355024.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPS2 | NM_001355024.4 | c.1448T>C | p.Ile483Thr | missense_variant | Exon 16 of 17 | ENST00000699294.1 | NP_001341953.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPS2 | ENST00000699294.1 | c.1448T>C | p.Ile483Thr | missense_variant | Exon 16 of 17 | NM_001355024.4 | ENSP00000514274.1 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000259 AC: 65AN: 251196Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135762
GnomAD4 exome AF: 0.000260 AC: 379AN: 1456322Hom.: 0 Cov.: 27 AF XY: 0.000292 AC XY: 212AN XY: 724976
GnomAD4 genome AF: 0.000263 AC: 40AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74378
ClinVar
Submissions by phenotype
not specified Benign:1
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