1-160190863-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001231.5(CASQ1):c.112C>T(p.Leu38=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000929 in 1,614,200 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 (★★).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000093 ( 0 hom. )
Consequence
CASQ1
NM_001231.5 synonymous
NM_001231.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.73
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 1-160190863-C-T is Benign according to our data. Variant chr1-160190863-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1568045.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CASQ1 | NM_001231.5 | c.112C>T | p.Leu38= | synonymous_variant | 1/11 | ENST00000368078.8 | NP_001222.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASQ1 | ENST00000368078.8 | c.112C>T | p.Leu38= | synonymous_variant | 1/11 | 1 | NM_001231.5 | ENSP00000357057 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152196Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251456Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135902
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GnomAD4 exome AF: 0.0000930 AC: 136AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.000103 AC XY: 75AN XY: 727248
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GnomAD4 genome AF: 0.0000919 AC: 14AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74474
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | CASQ1: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 12, 2024 | - - |
Computational scores
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Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at