chr10-66232072-C-G

Variant names:

• chr10-66232072-C-G
• rs1979363
• NM_013266.4:c.1884+48398G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

CTNNA3 Gene-Disease associations (from GenCC):

• arrhythmogenic right ventricular cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• arrhythmogenic right ventricular dysplasia 13

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• congenital heart disease

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CTNNA3	NM_013266.4	c.1884+48398G>C		intron_variant	Intron 13 of 17	ENST00000433211.7	NP_037398.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTNNA3	ENST00000433211.7	c.1884+48398G>C		intron_variant	Intron 13 of 17	1	NM_013266.4	ENSP00000389714.1

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

African (AFR) AF: 0.274 AC: 11367 AN: 41490

American (AMR) AF: 0.315 AC: 4804 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1311 AN: 3462

East Asian (EAS) AF: 0.459 AC: 2365 AN: 5154

South Asian (SAS) AF: 0.430 AC: 2068 AN: 4808

European-Finnish (FIN) AF: 0.418 AC: 4413 AN: 10546

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27185 AN: 67932

Other (OTH) AF: 0.349 AC: 737 AN: 2110

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
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1979363; hg19: chr10-67991830;