chr5-96722934-G-GTTGTT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001750.7(CAST):c.270+260_270+264dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 151,844 control chromosomes in the GnomAD database, including 566 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.062 ( 566 hom., cov: 31)
Consequence
CAST
NM_001750.7 intron
NM_001750.7 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.68
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 5-96722934-G-GTTGTT is Benign according to our data. Variant chr5-96722934-G-GTTGTT is described in ClinVar as [Benign]. Clinvar id is 1270998.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAST | NM_001750.7 | c.270+260_270+264dup | intron_variant | ENST00000675179.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAST | ENST00000675179.1 | c.270+260_270+264dup | intron_variant | NM_001750.7 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0625 AC: 9481AN: 151726Hom.: 563 Cov.: 31
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GnomAD4 genome ? AF: 0.0625 AC: 9489AN: 151844Hom.: 566 Cov.: 31 AF XY: 0.0648 AC XY: 4805AN XY: 74202
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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 20, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at