5-96689545-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001750.7(CAST):c.139-6291A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,090 control chromosomes in the GnomAD database, including 12,672 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (12672 hom., cov: 32)
• Consequence: CAST NM_001750.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAST	NM_001750.7	c.139-6291A>T		intron_variant		ENST00000675179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAST	ENST00000675179.1	c.139-6291A>T		intron_variant			NM_001750.7	A2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57570 AN: 151972 Hom.: 12633 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.379 AC: 57663 AN: 152090 Hom.: 12672 Cov.: 32 AF XY: 0.381 AC XY: 28314 AN XY: 74344

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.366

Alfa AF: 0.345 Hom.: 995

Bravo AF: 0.401

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs149319; hg19: chr5-96025249; COSMIC: COSV57783699;