rs7909676

chr10-66675039-C-Achr10-66675039-C-T

Variant summary

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

The NM_013266.4(CTNNA3):c.1282-53255G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,810 control chromosomes in the GnomAD database, including 24,002 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 0.55 (24002 hom., cov: 31)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA3	NM_013266.4	c.1282-53255G>T		intron_variant		ENST00000433211.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA3	ENST00000433211.7	c.1282-53255G>T		intron_variant		1	NM_013266.4	P1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83991 AN: 151692 Hom.: 23974 Cov.: 31

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.554 AC: 84066 AN: 151810 Hom.: 24002 Cov.: 31 AF XY: 0.551 AC XY: 40898 AN XY: 74174

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.547

Alfa AF: 0.536 Hom.: 2795

Bravo AF: 0.546

Asia WGS AF: 0.442 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.46
Dann	Benign	0.41

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: rs7909676; hg19: chr10-68434797;