rs2611713

Positions:

• chr5-96623246-G-A
• chr5-96623246-G-C

Variant summary

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

The NM_001423250.1(CAST):​c.-174-52293G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,032 control chromosomes in the GnomAD database, including 39,911 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 0.72 (39911 hom., cov: 31)
• Consequence: CAST NM_001423250.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAST	NM_001423250.1	c.-174-52293G>A		intron_variant			NP_001410179.1
CAST	NM_001423251.1	c.-174-52293G>A		intron_variant			NP_001410180.1
CAST	NM_001423252.1	c.-174-52293G>A		intron_variant			NP_001410181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAST	ENST00000505143.5	c.61-52293G>A		intron_variant		3		ENSP00000422957.2
ENSG00000251314	ENST00000502645.2	n.355-7721G>A		intron_variant		5
ENSG00000251314	ENST00000513158.1	n.542-7721G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109515 AN: 151914 Hom.: 39865 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.721 AC: 109612 AN: 152032 Hom.: 39911 Cov.: 31 AF XY: 0.723 AC XY: 53736 AN XY: 74302

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.706

Alfa AF: 0.694 Hom.: 74555

Bravo AF: 0.715

Asia WGS AF: 0.711 AC: 2475 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	0.32
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2611713; hg19: chr5-95958950;