2-30814619-T-C

Variant names:

• chr2-30814619-T-C
• rs6548038
• ENST00000465960.2:n.71+5853A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000465960.2(CAPN13):​n.71+5853A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,118 control chromosomes in the GnomAD database, including 39,725 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 0.72 (39725 hom., cov: 32)
• Consequence: CAPN13 ENST00000465960.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 6 publications found

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]

LOC124905982 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905982	XR_007086268.1	n.2731-5093A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAPN13	ENST00000465960.2	n.71+5853A>G		intron_variant	Intron 1 of 8	5

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109231 AN: 152000 Hom.: 39686 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.719 AC: 109321 AN: 152118 Hom.: 39725 Cov.: 32 AF XY: 0.716 AC XY: 53236 AN XY: 74366

African (AFR) AF: 0.792 AC: 32851 AN: 41480

American (AMR) AF: 0.557 AC: 8507 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2233 AN: 3472

East Asian (EAS) AF: 0.692 AC: 3583 AN: 5176

South Asian (SAS) AF: 0.633 AC: 3047 AN: 4816

European-Finnish (FIN) AF: 0.779 AC: 8242 AN: 10578

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48526 AN: 68000

Other (OTH) AF: 0.680 AC: 1437 AN: 2112

Alfa AF: 0.704 Hom.: 116102

Bravo AF: 0.702

Asia WGS AF: 0.676 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.55
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs6548038; hg19: chr2-31037485;