5-96729011-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001750.7(CAST):c.379-142A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 604,120 control chromosomes in the GnomAD database, including 15,811 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.19 (3085 hom., cov: 33)
  • Exomes 𝑓: 0.23 (12726 hom.)
• Consequence: CAST NM_001750.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.50

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 5-96729011-A-T is Benign according to our data. Variant chr5-96729011-A-T is described in ClinVar as [Benign]. Clinvar id is 1251790.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAST	NM_001750.7	c.379-142A>T		intron_variant		ENST00000675179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAST	ENST00000675179.1	c.379-142A>T		intron_variant			NM_001750.7	A2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28847 AN: 152076 Hom.: 3083 Cov.: 33

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.231 AC: 104338 AN: 451926 Hom.: 12726 Cov.: 4 AF XY: 0.232 AC XY: 55726 AN XY: 240518

Gnomad4 AFR exome AF: 0.0947

Gnomad4 AMR exome AF: 0.237

Gnomad4 ASJ exome AF: 0.155

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.248

Gnomad4 FIN exome AF: 0.267

Gnomad4 NFE exome AF: 0.221

Gnomad4 OTH exome AF: 0.210

GnomAD4 genome AF: 0.190 AC: 28845 AN: 152194 Hom.: 3085 Cov.: 33 AF XY: 0.195 AC XY: 14527 AN XY: 74404

Gnomad4 AFR AF: 0.0941

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.176

Alfa AF: 0.120 Hom.: 221

Bravo AF: 0.181

Asia WGS AF: 0.294 AC: 1025 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.7
Dann	Benign	0.66

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: rs28042; hg19: chr5-96064715; COSMIC: COSV57786632; COSMIC: COSV57786632;