5-96626125-C-T

Position:

• chr5-96626125-C-T

Variant summary

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

The NM_001423250.1(CAST):​c.-174-49414C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,156 control chromosomes in the GnomAD database, including 1,394 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 0.11 (1394 hom., cov: 32)
• Consequence: CAST NM_001423250.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

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]

CAST (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAST	NM_001423250.1	c.-174-49414C>T		intron_variant			NP_001410179.1
CAST	NM_001423251.1	c.-174-49414C>T		intron_variant			NP_001410180.1
CAST	NM_001423252.1	c.-174-49414C>T		intron_variant			NP_001410181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAST	ENST00000505143.5	c.61-49414C>T		intron_variant		3		ENSP00000422957.2
ENSG00000251314	ENST00000502645.2	n.355-4842C>T		intron_variant		5
ENSG00000251314	ENST00000513158.1	n.542-4842C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17342 AN: 152036 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.0322

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.114 AC: 17362 AN: 152156 Hom.: 1394 Cov.: 32 AF XY: 0.118 AC XY: 8772 AN XY: 74408

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.0945

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.116

Alfa AF: 0.122 Hom.: 1806

Bravo AF: 0.117

Asia WGS AF: 0.210 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515240; hg19: chr5-95961829;