rs1979363

chr10-66232072-C-G

Variant summary

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

The NM_013266.4(CTNNA3):c.1884+48398G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,978 control chromosomes in the GnomAD database, including 10,260 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 0.36 (10260 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA3	NM_013266.4	c.1884+48398G>C		intron_variant		ENST00000433211.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA3	ENST00000433211.7	c.1884+48398G>C		intron_variant		1	NM_013266.4	P1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54802 AN: 151860 Hom.: 10242 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.361 AC: 54857 AN: 151978 Hom.: 10260 Cov.: 32 AF XY: 0.364 AC XY: 27050 AN XY: 74262

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.349

Alfa AF: 0.374 Hom.: 1334

Bravo AF: 0.351

Asia WGS AF: 0.395 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.058
Dann	Benign	0.56

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: rs1979363; hg19: chr10-67991830;