2-30731755-C-T

Variant names:

• chr2-30731755-C-T
• rs540532
• NM_144575.3:c.1928-356G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144575.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPN13	NM_144575.3	MANE Select	c.1928-356G>A		intron	N/A	NP_653176.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPN13	ENST00000295055.12	TSL:5 MANE Select	c.1928-356G>A		intron	N/A	ENSP00000295055.8	Q6MZZ7-1
	CAPN13	ENST00000946473.1		c.1928-356G>A		intron	N/A	ENSP00000616532.1
	CAPN13	ENST00000946475.1		c.1928-356G>A		intron	N/A	ENSP00000616534.1

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

African (AFR) AF: 0.926 AC: 38474 AN: 41554

American (AMR) AF: 0.683 AC: 10451 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2894 AN: 3472

East Asian (EAS) AF: 0.725 AC: 3741 AN: 5160

South Asian (SAS) AF: 0.733 AC: 3531 AN: 4814

European-Finnish (FIN) AF: 0.871 AC: 9236 AN: 10602

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56071 AN: 68014

Other (OTH) AF: 0.813 AC: 1718 AN: 2112

Alfa AF: 0.823 Hom.: 12519

Bravo AF: 0.824

Asia WGS AF: 0.750 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.58
DANN	Benign	0.51
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs540532; hg19: chr2-30954621;