10-67072658-C-T

Variant summary

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

The NM_013266.4(CTNNA3):c.1047+107659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,946 control chromosomes in the GnomAD database, including 9,624 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 0.35 (9624 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

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]

LRRTM3 (HGNC:19410): (leucine rich repeat transmembrane neuronal 3) Involved in presynapse assembly. Acts upstream of or within positive regulation of amyloid-beta formation. Is active in glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA3	NM_013266.4	c.1047+107659G>A		intron_variant		ENST00000433211.7
LRRTM3	NM_178011.5	c.1537-24929C>T		intron_variant		ENST00000361320.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRTM3	ENST00000361320.5	c.1537-24929C>T		intron_variant		1	NM_178011.5	P1
CTNNA3	ENST00000433211.7	c.1047+107659G>A		intron_variant		1	NM_013266.4	P1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52591 AN: 151830 Hom.: 9622 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.346 AC: 52600 AN: 151946 Hom.: 9624 Cov.: 32 AF XY: 0.346 AC XY: 25676 AN XY: 74248

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.381

Alfa AF: 0.344 Hom.: 4346

Bravo AF: 0.344

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.8
Dann	Benign	0.63

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: rs2619652; hg19: chr10-68832416;