NM_000070.3:c.1227A>C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6BP7
The NM_000070.3(CAPN3):āc.1227A>Cā(p.Thr409Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,894 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T409T) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPN3 | NM_000070.3 | c.1227A>C | p.Thr409Thr | synonymous_variant | Exon 10 of 24 | ENST00000397163.8 | NP_000061.1 | |
CAPN3 | NM_024344.2 | c.1227A>C | p.Thr409Thr | synonymous_variant | Exon 10 of 23 | NP_077320.1 | ||
CAPN3 | NM_173087.2 | c.1083A>C | p.Thr361Thr | synonymous_variant | Exon 9 of 21 | NP_775110.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN3 | ENST00000397163.8 | c.1227A>C | p.Thr409Thr | synonymous_variant | Exon 10 of 24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
ENSG00000258461 | ENST00000495723.1 | n.*1023A>C | non_coding_transcript_exon_variant | Exon 14 of 26 | 2 | ENSP00000492063.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*1023A>C | 3_prime_UTR_variant | Exon 14 of 26 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152070Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251464Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135906
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461706Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727164
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152188Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74396
ClinVar
Submissions by phenotype
not provided Uncertain:1
- -
not specified Benign:1
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Autosomal recessive limb-girdle muscular dystrophy type 2A Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at