rs9314177

Positions:

• chr5-96693156-A-G
• chr5-96693156-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.139-2680A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,098 control chromosomes in the GnomAD database, including 26,406 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 0.58 (26406 hom., cov: 32)
• Consequence: CAST NM_001750.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

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=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAST	NM_001750.7	c.139-2680A>G		intron_variant		ENST00000675179.1	NP_001741.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAST	ENST00000675179.1	c.139-2680A>G		intron_variant			NM_001750.7	ENSP00000501872	A2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 88050 AN: 151980 Hom.: 26410 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.579 AC: 88067 AN: 152098 Hom.: 26406 Cov.: 32 AF XY: 0.579 AC XY: 43009 AN XY: 74336

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.597

Alfa AF: 0.646 Hom.: 42007

Bravo AF: 0.563

Asia WGS AF: 0.532 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	7.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9314177; hg19: chr5-96028860;