15-42359811-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000070.3(CAPN3):c.6G>T(p.Pro2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000308 in 1,461,238 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P2P) has been classified as Likely benign.
Frequency
Consequence
NM_000070.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAPN3 | NM_000070.3 | c.6G>T | p.Pro2= | synonymous_variant | 1/24 | ENST00000397163.8 | |
CAPN3 | NM_024344.2 | c.6G>T | p.Pro2= | synonymous_variant | 1/23 | ||
CAPN3 | NM_173087.2 | c.6G>T | p.Pro2= | synonymous_variant | 1/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAPN3 | ENST00000397163.8 | c.6G>T | p.Pro2= | synonymous_variant | 1/24 | 1 | NM_000070.3 | P2 | |
CAPN3 | ENST00000357568.8 | c.6G>T | p.Pro2= | synonymous_variant | 1/23 | 1 | |||
CAPN3 | ENST00000349748.8 | c.6G>T | p.Pro2= | synonymous_variant | 1/21 | 1 | |||
CAPN3 | ENST00000318023.11 | c.6G>T | p.Pro2= | synonymous_variant | 1/23 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250300Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135720
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461238Hom.: 0 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 726936
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at