15-42384491-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_000070.3(CAPN3):c.318C>T(p.Cys106Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00573 in 1,612,482 control chromosomes in the GnomAD database, including 34 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPN3 | NM_000070.3 | c.318C>T | p.Cys106Cys | synonymous_variant | Exon 2 of 24 | ENST00000397163.8 | NP_000061.1 | |
CAPN3 | NM_024344.2 | c.318C>T | p.Cys106Cys | synonymous_variant | Exon 2 of 23 | NP_077320.1 | ||
CAPN3 | NM_173087.2 | c.318C>T | p.Cys106Cys | synonymous_variant | Exon 2 of 21 | NP_775110.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN3 | ENST00000397163.8 | c.318C>T | p.Cys106Cys | synonymous_variant | Exon 2 of 24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
ENSG00000258461 | ENST00000495723.1 | n.*114C>T | non_coding_transcript_exon_variant | Exon 6 of 26 | 2 | ENSP00000492063.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*114C>T | 3_prime_UTR_variant | Exon 6 of 26 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes AF: 0.00488 AC: 743AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00470 AC: 1182AN: 251426Hom.: 5 AF XY: 0.00475 AC XY: 646AN XY: 135878
GnomAD4 exome AF: 0.00582 AC: 8494AN: 1460228Hom.: 34 Cov.: 30 AF XY: 0.00570 AC XY: 4142AN XY: 726566
GnomAD4 genome AF: 0.00487 AC: 742AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.00450 AC XY: 335AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:5
p.Cys106Cys in exon 2 of CAPN3: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 0.9% (78/8598) of European American chromosomes from a broad population by the NHLBI Exome Sequenc ing Project (http://evs.gs.washington.edu/EVS; dbSNP rs117609395). -
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not provided Benign:4
CAPN3: BP4, BP7, BS2 -
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This variant is associated with the following publications: (PMID: 10330340, 16141003) -
Autosomal recessive limb-girdle muscular dystrophy type 2A Benign:3
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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at