rs3838216
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001231.5(CASQ1):c.279+813_279+814insGGCATTCAGATAGGCCT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 9618 hom., cov: 0)
Consequence
CASQ1
NM_001231.5 intron
NM_001231.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.01
Genes affected
CASQ1 (HGNC:1512): (calsequestrin 1) This gene encodes the skeletal muscle specific member of the calsequestrin protein family. Calsequestrin functions as a luminal sarcoplasmic reticulum calcium sensor in both cardiac and skeletal muscle cells. This protein, also known as calmitine, functions as a calcium regulator in the mitochondria of skeletal muscle. This protein is absent in patients with Duchenne and Becker types of muscular dystrophy. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CASQ1 | NM_001231.5 | c.279+813_279+814insGGCATTCAGATAGGCCT | intron_variant | ENST00000368078.8 | NP_001222.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASQ1 | ENST00000368078.8 | c.279+813_279+814insGGCATTCAGATAGGCCT | intron_variant | 1 | NM_001231.5 | ENSP00000357057.3 |
Frequencies
GnomAD3 genomes AF: 0.320 AC: 48594AN: 152036Hom.: 9589 Cov.: 0
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GnomAD4 genome AF: 0.320 AC: 48662AN: 152156Hom.: 9618 Cov.: 0 AF XY: 0.315 AC XY: 23456AN XY: 74398
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3478
ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at