10-67095222-T-C

Variant names:

• chr10-67095222-T-C
• rs12785206
• NM_013266.4:c.1047+85095A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

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

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNNA3	NM_013266.4	MANE Select	c.1047+85095A>G		intron	N/A	NP_037398.2	Q9UI47-1
	LRRTM3	NM_178011.5	MANE Select	c.1537-2365T>C		intron	N/A	NP_821079.3
	CTNNA3	NM_001127384.3		c.1047+85095A>G		intron	N/A	NP_001120856.1	Q9UI47-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNNA3	ENST00000433211.7	TSL:1 MANE Select	c.1047+85095A>G		intron	N/A	ENSP00000389714.1	Q9UI47-1
	LRRTM3	ENST00000361320.5	TSL:1 MANE Select	c.1537-2365T>C		intron	N/A	ENSP00000355187.3	Q86VH5-1
	CTNNA3	ENST00000682758.1		c.1047+85095A>G		intron	N/A	ENSP00000508047.1	Q9UI47-1

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

African (AFR) AF: 0.0980 AC: 4064 AN: 41486

American (AMR) AF: 0.284 AC: 4291 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3466

East Asian (EAS) AF: 0.260 AC: 1333 AN: 5136

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4810

European-Finnish (FIN) AF: 0.371 AC: 3907 AN: 10534

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22013 AN: 67612

Other (OTH) AF: 0.288 AC: 603 AN: 2096

Alfa AF: 0.314 Hom.: 9628

Bravo AF: 0.252

Asia WGS AF: 0.247 AC: 856 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		0.11
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: rs12785206; hg19: chr10-68854980;