rs149313

chr5-96734501-T-Cchr5-96734501-T-G

Variant summary

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

The NM_001750.7(CAST):c.631-1671T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,040 control chromosomes in the GnomAD database, including 20,064 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 0.51 (20064 hom., cov: 32)
• Consequence: CAST NM_001750.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAST	NM_001750.7	c.631-1671T>C		intron_variant		ENST00000675179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAST	ENST00000675179.1	c.631-1671T>C		intron_variant			NM_001750.7	A2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77954 AN: 151922 Hom.: 20048 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.513 AC: 78014 AN: 152040 Hom.: 20064 Cov.: 32 AF XY: 0.512 AC XY: 38029 AN XY: 74298

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.484

Alfa AF: 0.529 Hom.: 43539

Bravo AF: 0.508

Asia WGS AF: 0.508 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.6
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs149313; hg19: chr5-96070205;