rs1925613

chr10-67002986-C-Achr10-67002986-C-G

Variant summary

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

The NM_013266.4(CTNNA3):c.1047+177331G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,964 control chromosomes in the GnomAD database, including 20,476 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 0.51 (20476 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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]

LOC101928961 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA3	NM_013266.4	c.1047+177331G>T		intron_variant		ENST00000433211.7
LRRTM3	NM_178011.5	c.1536+74534C>A		intron_variant		ENST00000361320.5
LOC101928961	NR_111911.1	n.91+9077G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRTM3	ENST00000361320.5	c.1536+74534C>A		intron_variant		1	NM_178011.5	P1
CTNNA3	ENST00000433211.7	c.1047+177331G>T		intron_variant		1	NM_013266.4	P1

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77128 AN: 151846 Hom.: 20476 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.508 AC: 77151 AN: 151964 Hom.: 20476 Cov.: 32 AF XY: 0.510 AC XY: 37879 AN XY: 74266

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.557

Alfa AF: 0.551 Hom.: 13378

Bravo AF: 0.490

Asia WGS AF: 0.428 AC: 1488 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	2.7
Dann	Benign	0.78

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: rs1925613; hg19: chr10-68762744;