chr2-30731755-C-T

Position:

• chr2-30731755-C-T

Variant summary

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

The NM_144575.3(CAPN13):​c.1928-356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,228 control chromosomes in the GnomAD database, including 53,558 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 0.84 (53558 hom., cov: 33)
• Consequence: CAPN13 NM_144575.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517

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]

CAPN13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAPN13	NM_144575.3	c.1928-356G>A		intron_variant		ENST00000295055.12	NP_653176.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAPN13	ENST00000295055.12	c.1928-356G>A		intron_variant		5	NM_144575.3	ENSP00000295055.8
CAPN13	ENST00000450650.5	n.*1373-356G>A		intron_variant		2		ENSP00000403180.1
CAPN13	ENST00000490786.1	n.48-356G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.835 AC: 127008 AN: 152110 Hom.: 53497 Cov.: 33

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.835 AC: 127126 AN: 152228 Hom.: 53558 Cov.: 33 AF XY: 0.830 AC XY: 61802 AN XY: 74418

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.813

Alfa AF: 0.821 Hom.: 12186

Bravo AF: 0.824

Asia WGS AF: 0.750 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.58
DANN	Benign	0.51

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: rs540532; hg19: chr2-30954621;