19-38767470-C-T

Position:

• chr19-38767470-C-T

Variant summary

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

The ENST00000601953.5(CAPN12):​c.-141+2328G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,874 control chromosomes in the GnomAD database, including 13,025 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 0.41 (13025 hom., cov: 31)
• Consequence: CAPN12 ENST00000601953.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26

Genes affected

CAPN12 (HGNC:13249): (calpain 12) The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes a member of the calpain large subunit family. [provided by RefSeq, Jun 2012]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38767470C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAPN12	ENST00000601953.5	c.-141+2328G>A		intron_variant		5		ENSP00000473156.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61773 AN: 151756 Hom.: 13012 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.407 AC: 61802 AN: 151874 Hom.: 13025 Cov.: 31 AF XY: 0.404 AC XY: 30027 AN XY: 74238

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.398

Alfa AF: 0.435 Hom.: 21522

Bravo AF: 0.391

Asia WGS AF: 0.244 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7248584; hg19: chr19-39258110;