rs13388696

chr2-30726801-G-Cchr2-30726801-G-T

Variant summary

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

The NM_144575.3(CAPN13):c.*31-3565C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,930 control chromosomes in the GnomAD database, including 15,497 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 0.45 (15497 hom., cov: 32)
• Consequence: CAPN13 NM_144575.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

CAPN13 (HGNC:16663): (calpain 13) 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPN13	NM_144575.3	c.*31-3565C>G		intron_variant		ENST00000295055.12
CAPN13	XM_011533161.4	c.*609C>G		3_prime_UTR_variant	23/23
CAPN13	XM_047446332.1	c.*31-1904C>G		intron_variant
CAPN13	XR_939741.4	n.2898C>G		non_coding_transcript_exon_variant	24/24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPN13	ENST00000295055.12	c.*31-3565C>G		intron_variant		5	NM_144575.3	P1
CAPN13	ENST00000450650.5	c.*1486-3565C>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68095 AN: 151812 Hom.: 15478 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.449 AC: 68152 AN: 151930 Hom.: 15497 Cov.: 32 AF XY: 0.449 AC XY: 33315 AN XY: 74264

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.447

Alfa AF: 0.290 Hom.: 703

Bravo AF: 0.447

Asia WGS AF: 0.586 AC: 2034 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.1
Dann	Benign	0.65

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: rs13388696; hg19: chr2-30949667;