rs1801505
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000070.3(CAPN3):c.319G>A(p.Glu107Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00855 in 1,613,074 control chromosomes in the GnomAD database, including 93 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 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPN3 | NM_000070.3 | c.319G>A | p.Glu107Lys | missense_variant | Exon 2 of 24 | ENST00000397163.8 | NP_000061.1 | |
CAPN3 | NM_024344.2 | c.319G>A | p.Glu107Lys | missense_variant | Exon 2 of 23 | NP_077320.1 | ||
CAPN3 | NM_173087.2 | c.319G>A | p.Glu107Lys | missense_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.319G>A | p.Glu107Lys | missense_variant | Exon 2 of 24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
ENSG00000258461 | ENST00000495723.1 | n.*115G>A | non_coding_transcript_exon_variant | Exon 6 of 26 | 2 | ENSP00000492063.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*115G>A | 3_prime_UTR_variant | Exon 6 of 26 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes AF: 0.00672 AC: 1022AN: 152118Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00853 AC: 2146AN: 251436Hom.: 22 AF XY: 0.00823 AC XY: 1118AN XY: 135892
GnomAD4 exome AF: 0.00874 AC: 12767AN: 1460838Hom.: 82 Cov.: 30 AF XY: 0.00847 AC XY: 6158AN XY: 726816
GnomAD4 genome AF: 0.00671 AC: 1022AN: 152236Hom.: 11 Cov.: 32 AF XY: 0.00674 AC XY: 502AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:5
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p.Glu107Lys in exon 2 of CAPN3: This variant is not expected to have clinical si gnificance because it has been identified in 2.8% (188/66736) of European (Finni sh) chromosomes including 2 homozygotes by the Exome Aggregation Consortium (ExA C, http://exac.broadinstitute.org; dbSNP rs150616566) -
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. -
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not provided Benign:4
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CAPN3: BS1, BS2 -
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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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
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Autosomal recessive limb-girdle muscular dystrophy type 2A;C4748295:Muscular dystrophy, limb-girdle, autosomal dominant 4 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at