rs1801449
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000070.3(CAPN3):c.706G>A(p.Ala236Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0836 in 1,613,710 control chromosomes in the GnomAD database, including 19,097 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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CAPN3 | NM_000070.3 | c.706G>A | p.Ala236Thr | missense_variant | Exon 5 of 24 | ENST00000397163.8 | NP_000061.1 | |
CAPN3 | NM_024344.2 | c.706G>A | p.Ala236Thr | missense_variant | Exon 5 of 23 | NP_077320.1 | ||
CAPN3 | NM_173087.2 | c.706G>A | p.Ala236Thr | missense_variant | Exon 5 of 21 | NP_775110.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN3 | ENST00000397163.8 | c.706G>A | p.Ala236Thr | missense_variant | Exon 5 of 24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
ENSG00000258461 | ENST00000495723.1 | n.*502G>A | non_coding_transcript_exon_variant | Exon 9 of 26 | 2 | ENSP00000492063.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*502G>A | 3_prime_UTR_variant | Exon 9 of 26 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes AF: 0.222 AC: 33668AN: 151864Hom.: 8632 Cov.: 31
GnomAD3 exomes AF: 0.113 AC: 28526AN: 251464Hom.: 4356 AF XY: 0.106 AC XY: 14383AN XY: 135906
GnomAD4 exome AF: 0.0692 AC: 101133AN: 1461728Hom.: 10430 Cov.: 32 AF XY: 0.0698 AC XY: 50733AN XY: 727158
GnomAD4 genome AF: 0.222 AC: 33763AN: 151982Hom.: 8667 Cov.: 31 AF XY: 0.219 AC XY: 16236AN XY: 74296
ClinVar
Submissions by phenotype
not specified Benign:7
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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. -
p.Ala236Thr in exon 5 of CAPN3: This variant is not expected to have clinical si gnificance because it has been identified in 62% (2737/4406) of African American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu /EVS/; dbSNP rs1801449). -
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Autosomal recessive limb-girdle muscular dystrophy type 2A Benign:6
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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 was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
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not provided Benign:2
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Muscular dystrophy, limb-girdle, autosomal dominant 4 Benign:1
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Limb-girdle muscular dystrophy, recessive Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at