rs1786909

chr10-65940412-A-Cchr10-65940412-A-T

Variant summary

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

The NM_013266.4(CTNNA3):c.2401-19795T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,112 control chromosomes in the GnomAD database, including 48,726 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 0.80 (48726 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA3	NM_013266.4	c.2401-19795T>G		intron_variant		ENST00000433211.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA3	ENST00000433211.7	c.2401-19795T>G		intron_variant		1	NM_013266.4	P1

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121371 AN: 151994 Hom.: 48680 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.799 AC: 121472 AN: 152112 Hom.: 48726 Cov.: 32 AF XY: 0.799 AC XY: 59436 AN XY: 74364

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.819

Alfa AF: 0.773 Hom.: 74648

Bravo AF: 0.804

Asia WGS AF: 0.789 AC: 2746 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	1.5
Dann	Benign	0.54

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: rs1786909; hg19: chr10-67700170;