rs2368524

Variant names:

• chr19-38761598-G-A
• rs2368524
• ENST00000601953.5:c.-141+8200C>T

Variant summary

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

The ENST00000601953.5(CAPN12):​c.-141+8200C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,930 control chromosomes in the GnomAD database, including 967 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 (967 hom., cov: 32)
• Consequence: CAPN12 ENST00000601953.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAPN12	ENST00000601953.5	c.-141+8200C>T		intron_variant	Intron 1 of 19	5		ENSP00000473156.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16080 AN: 151812 Hom.: 969 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.106 AC: 16102 AN: 151930 Hom.: 967 Cov.: 32 AF XY: 0.106 AC XY: 7888 AN XY: 74254

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.0436

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.0867

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0906 Hom.: 246

Bravo AF: 0.115

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2368524; hg19: chr19-39252238;