chr10-67095222-T-C

Position:

• chr10-67095222-T-C

Variant summary

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

The NM_013266.4(CTNNA3):​c.1047+85095A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,478 control chromosomes in the GnomAD database, including 6,033 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 0.26 (6033 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNA3	NM_013266.4	c.1047+85095A>G		intron_variant		ENST00000433211.7	NP_037398.2
LRRTM3	NM_178011.5	c.1537-2365T>C		intron_variant		ENST00000361320.5	NP_821079.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRTM3	ENST00000361320.5	c.1537-2365T>C		intron_variant		1	NM_178011.5	ENSP00000355187	P1
CTNNA3	ENST00000433211.7	c.1047+85095A>G		intron_variant		1	NM_013266.4	ENSP00000389714	P1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39338 AN: 151360 Hom.: 6030 Cov.: 32

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.260 AC: 39339 AN: 151478 Hom.: 6033 Cov.: 32 AF XY: 0.261 AC XY: 19293 AN XY: 73964

Gnomad4 AFR AF: 0.0980

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.288

Alfa AF: 0.323 Hom.: 7816

Bravo AF: 0.252

Asia WGS AF: 0.247 AC: 856 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.7
DANN	Benign	0.82

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: rs12785206; hg19: chr10-68854980;