chr10-65983896-A-T

Variant names:

• chr10-65983896-A-T
• rs72791417
• NM_013266.4:c.2265+4796T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013266.4(CTNNA3):​c.2265+4796T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,244 control chromosomes in the GnomAD database, including 1,380 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 0.11 (1380 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTNNA3	NM_013266.4	c.2265+4796T>A		intron_variant	Intron 16 of 17	ENST00000433211.7	NP_037398.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTNNA3	ENST00000433211.7	c.2265+4796T>A		intron_variant	Intron 16 of 17	1	NM_013266.4	ENSP00000389714.1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17319 AN: 151126 Hom.: 1377 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.115 AC: 17325 AN: 151244 Hom.: 1380 Cov.: 32 AF XY: 0.123 AC XY: 9118 AN XY: 73914

African (AFR) AF: 0.0321 AC: 1331 AN: 41504

American (AMR) AF: 0.170 AC: 2584 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 404 AN: 3450

East Asian (EAS) AF: 0.174 AC: 896 AN: 5154

South Asian (SAS) AF: 0.251 AC: 1208 AN: 4820

European-Finnish (FIN) AF: 0.242 AC: 2539 AN: 10490

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 290

European-Non Finnish (NFE) AF: 0.119 AC: 7989 AN: 67356

Other (OTH) AF: 0.109 AC: 229 AN: 2096

Alfa AF: 0.118 Hom.: 166

Bravo AF: 0.106

Asia WGS AF: 0.219 AC: 759 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		0.64
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: rs72791417; hg19: chr10-67743654;