rs7923367

Variant names:

• chr10-67413145-G-A
• rs7923367
• NM_013266.4:c.579+108697C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-67413145-G-A
• chr10-67413145-G-C
• chr10-67413145-G-T

Variant summary

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

The NM_013266.4(CTNNA3):​c.579+108697C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0688 in 151,888 control chromosomes in the GnomAD database, including 500 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 0.069 (500 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013266.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNNA3	NM_013266.4	MANE Select	c.579+108697C>T		intron	N/A	NP_037398.2
	CTNNA3	NM_001127384.3		c.579+108697C>T		intron	N/A	NP_001120856.1
	CTNNA3	NM_001291133.2		c.615+108697C>T		intron	N/A	NP_001278062.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNNA3	ENST00000433211.7	TSL:1 MANE Select	c.579+108697C>T		intron	N/A	ENSP00000389714.1
	CTNNA3	ENST00000682758.1		c.579+108697C>T		intron	N/A	ENSP00000508047.1
	CTNNA3	ENST00000684154.1		c.579+108697C>T		intron	N/A	ENSP00000508371.1

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10429 AN: 151770 Hom.: 496 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.0369

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0688 AC: 10453 AN: 151888 Hom.: 500 Cov.: 32 AF XY: 0.0684 AC XY: 5079 AN XY: 74212

African (AFR) AF: 0.138 AC: 5703 AN: 41430

American (AMR) AF: 0.0508 AC: 774 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0453 AC: 157 AN: 3464

East Asian (EAS) AF: 0.00521 AC: 27 AN: 5182

South Asian (SAS) AF: 0.0977 AC: 469 AN: 4800

European-Finnish (FIN) AF: 0.0369 AC: 390 AN: 10560

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0411 AC: 2792 AN: 67898

Other (OTH) AF: 0.0569 AC: 120 AN: 2110

Alfa AF: 0.0355 Hom.: 52

Bravo AF: 0.0697

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		-0.85
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: rs7923367; hg19: chr10-69172903;