rs138867099
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000070.3(CAPN3):c.232C>A(p.Pro78Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000235 in 1,614,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000070.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPN3 | NM_000070.3 | c.232C>A | p.Pro78Thr | missense_variant | Exon 1 of 24 | ENST00000397163.8 | NP_000061.1 | |
CAPN3 | NM_024344.2 | c.232C>A | p.Pro78Thr | missense_variant | Exon 1 of 23 | NP_077320.1 | ||
CAPN3 | NM_173087.2 | c.232C>A | p.Pro78Thr | missense_variant | Exon 1 of 21 | NP_775110.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN3 | ENST00000397163.8 | c.232C>A | p.Pro78Thr | missense_variant | Exon 1 of 24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
ENSG00000258461 | ENST00000495723.1 | n.*105+5584C>A | intron_variant | Intron 5 of 25 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes AF: 0.000315 AC: 48AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000385 AC: 96AN: 249514Hom.: 0 AF XY: 0.000474 AC XY: 64AN XY: 135008
GnomAD4 exome AF: 0.000227 AC: 332AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.000259 AC XY: 188AN XY: 727230
GnomAD4 genome AF: 0.000315 AC: 48AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74480
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2A Uncertain:3Benign:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
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not provided Uncertain:1Benign:1
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Reported previously in an individual undergoing next generation sequencing testing for myopathy, although further information was not provided on this individual (Di Fruscio et al., 2016); This variant is associated with the following publications: (PMID: 25898921) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at