rs1909655

chr10-67618782-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.100-11733A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 152,232 control chromosomes in the GnomAD database, including 916 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 0.090 (916 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA3	NM_013266.4	c.100-11733A>G		intron_variant		ENST00000433211.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA3	ENST00000433211.7	c.100-11733A>G		intron_variant		1	NM_013266.4	P1

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13722 AN: 152112 Hom.: 914 Cov.: 32

Gnomad AFR AF: 0.0193

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0612

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0901 AC: 13722 AN: 152232 Hom.: 916 Cov.: 32 AF XY: 0.0961 AC XY: 7151 AN XY: 74438

Gnomad4 AFR AF: 0.0192

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0612

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.0928

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0960 Hom.: 618

Bravo AF: 0.0815

Asia WGS AF: 0.166 AC: 578 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	15
Dann	Benign	0.91

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: rs1909655; hg19: chr10-69378540;