chr5-96662653-G-GGCAGGTGGCT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001750.7(CAST):c.75+167_75+176dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.29 ( 6951 hom., cov: 0)
Consequence
CAST
NM_001750.7 intron
NM_001750.7 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.132
Genes affected
CAST (HGNC:1515): (calpastatin) The protein encoded by this gene is an endogenous calpain (calcium-dependent cysteine protease) inhibitor. It consists of an N-terminal domain L and four repetitive calpain-inhibition domains (domains 1-4), and it is involved in the proteolysis of amyloid precursor protein. The calpain/calpastatin system is involved in numerous membrane fusion events, such as neural vesicle exocytosis and platelet and red-cell aggregation. The encoded protein is also thought to affect the expression levels of genes encoding structural or regulatory proteins. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 5-96662653-G-GGCAGGTGGCT is Benign according to our data. Variant chr5-96662653-G-GGCAGGTGGCT is described in ClinVar as [Benign]. Clinvar id is 1247631.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAST | NM_001750.7 | c.75+167_75+176dup | intron_variant | ENST00000675179.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAST | ENST00000675179.1 | c.75+167_75+176dup | intron_variant | NM_001750.7 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.292 AC: 44346AN: 151646Hom.: 6943 Cov.: 0
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GnomAD4 genome ? AF: 0.292 AC: 44371AN: 151758Hom.: 6951 Cov.: 0 AF XY: 0.298 AC XY: 22081AN XY: 74156
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at