rs62642519
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000070.3(CAPN3):c.78G>A(p.Pro26Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00302 in 1,614,128 control chromosomes in the GnomAD database, including 127 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000070.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPN3 | NM_000070.3 | c.78G>A | p.Pro26Pro | synonymous_variant | Exon 1 of 24 | ENST00000397163.8 | NP_000061.1 | |
CAPN3 | NM_024344.2 | c.78G>A | p.Pro26Pro | synonymous_variant | Exon 1 of 23 | NP_077320.1 | ||
CAPN3 | NM_173087.2 | c.78G>A | p.Pro26Pro | synonymous_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.78G>A | p.Pro26Pro | synonymous_variant | Exon 1 of 24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
ENSG00000258461 | ENST00000495723.1 | n.*105+5430G>A | intron_variant | Intron 5 of 25 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes AF: 0.0167 AC: 2535AN: 152144Hom.: 73 Cov.: 32
GnomAD3 exomes AF: 0.00389 AC: 977AN: 251062Hom.: 27 AF XY: 0.00286 AC XY: 389AN XY: 135828
GnomAD4 exome AF: 0.00160 AC: 2339AN: 1461868Hom.: 53 Cov.: 32 AF XY: 0.00134 AC XY: 977AN XY: 727234
GnomAD4 genome AF: 0.0167 AC: 2541AN: 152260Hom.: 74 Cov.: 32 AF XY: 0.0165 AC XY: 1228AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Autosomal recessive limb-girdle muscular dystrophy type 2A Benign:3
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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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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Limb-girdle muscular dystrophy, recessive Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at