2-240594824-AGATGATTCTGTCCCAGGAGCCGGGAGGAGGGT-AGATGATTCTGTCCCAGGAGCCGGGAGGAGGGTGATGATTCTGTCCCAGGAGCCGGGAGGAGGGT
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_023083.4(CAPN10):c.997+136_998-148dupCGGGAGGAGGGTGATGATTCTGTCCCAGGAGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 791,422 control chromosomes in the GnomAD database, including 89,362 homozygotes. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.49 ( 18630 hom., cov: 37)
Exomes 𝑓: 0.37 ( 70732 hom. )
Consequence
CAPN10
NM_023083.4 intron
NM_023083.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0430
Genes affected
CAPN10 (HGNC:1477): (calpain 10) Calpains represent a ubiquitous, well-conserved family of calcium-dependent cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large catalytic subunit has four domains: domain I, the N-terminal regulatory domain that is processed upon calpain activation; domain II, the protease domain; domain III, a linker domain of unknown function; and domain IV, the calmodulin-like calcium-binding domain. This gene encodes a large subunit. It is an atypical calpain in that it lacks the calmodulin-like calcium-binding domain and instead has a divergent C-terminal domain. It is similar in organization to calpains 5 and 6. This gene is associated with type 2 or non-insulin-dependent diabetes mellitus (NIDDM), and is located within the NIDDM1 region. Multiple alternative transcript variants have been described for this gene. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPN10 | NM_023083.4 | c.997+136_998-148dupCGGGAGGAGGGTGATGATTCTGTCCCAGGAGC | intron_variant | ENST00000391984.7 | NP_075571.2 | |||
CAPN10 | NM_023085.4 | c.997+136_998-148dupCGGGAGGAGGGTGATGATTCTGTCCCAGGAGC | intron_variant | NP_075573.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.492 AC: 66138AN: 134404Hom.: 18616 Cov.: 37
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GnomAD4 exome AF: 0.375 AC: 246097AN: 656900Hom.: 70732 AF XY: 0.386 AC XY: 129400AN XY: 335262
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GnomAD4 genome AF: 0.492 AC: 66183AN: 134522Hom.: 18630 Cov.: 37 AF XY: 0.488 AC XY: 31591AN XY: 64722
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ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Type 2 diabetes mellitus 1, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 01, 2002 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at