rs2456751

Positions:

• chr10-66405295-T-C

Variant summary

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

The NM_013266.4(CTNNA3):​c.1532-25943A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,926 control chromosomes in the GnomAD database, including 31,725 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 0.63 (31725 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824

Genes affected

CTNNA3 (HGNC:2511): (catenin alpha 3) This gene encodes a protein that belongs to the vinculin/alpha-catenin family. The encoded protein plays a role in cell-cell adhesion in muscle cells. Mutations in this gene are associated with arrhythmogenic right ventricular dysplasia, familial 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNA3	NM_013266.4	c.1532-25943A>G		intron_variant		ENST00000433211.7	NP_037398.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNNA3	ENST00000433211.7	c.1532-25943A>G		intron_variant		1	NM_013266.4	ENSP00000389714	P1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95469 AN: 151808 Hom.: 31676 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.629 AC: 95577 AN: 151926 Hom.: 31725 Cov.: 32 AF XY: 0.630 AC XY: 46785 AN XY: 74208

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.634

Alfa AF: 0.562 Hom.: 3160

Bravo AF: 0.641

Asia WGS AF: 0.854 AC: 2968 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.66

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: rs2456751; hg19: chr10-68165053;