2-30814619-T-C

Variant summary

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

The XR_007086268.1(LOC124905982):n.2731-5093A>G variant causes a intron, non coding transcript 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: LOC124905982 XR_007086268.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

LOC124905982 (HGNC:):

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=-0.91).
• 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/exons	MANE	UniProt
LOC124905982	XR_007086268.1	n.2731-5093A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPN13	ENST00000465960.2	n.71+5853A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.680

Alfa AF: 0.700 Hom.: 74988

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6548038; hg19: chr2-31037485;