rs6480245

Variant names:

• chr10-66987233-G-A
• rs6480245
• NM_013266.4:c.1047+193084C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-66987233-G-A
• chr10-66987233-G-C
• chr10-66987233-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.1047+193084C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,064 control chromosomes in the GnomAD database, including 38,423 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 0.71 (38423 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• 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]

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]

ENSG00000302985 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTNNA3	NM_013266.4	c.1047+193084C>T		intron_variant	Intron 7 of 17	ENST00000433211.7	NP_037398.2
LRRTM3	NM_178011.5	c.1536+58781G>A		intron_variant	Intron 2 of 2	ENST00000361320.5	NP_821079.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTNNA3	ENST00000433211.7	c.1047+193084C>T		intron_variant	Intron 7 of 17	1	NM_013266.4	ENSP00000389714.1
LRRTM3	ENST00000361320.5	c.1536+58781G>A		intron_variant	Intron 2 of 2	1	NM_178011.5	ENSP00000355187.3

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107745 AN: 151946 Hom.: 38385 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.709 AC: 107835 AN: 152064 Hom.: 38423 Cov.: 32 AF XY: 0.709 AC XY: 52667 AN XY: 74304

African (AFR) AF: 0.757 AC: 31398 AN: 41500

American (AMR) AF: 0.752 AC: 11495 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3466

East Asian (EAS) AF: 0.803 AC: 4149 AN: 5168

South Asian (SAS) AF: 0.747 AC: 3597 AN: 4816

European-Finnish (FIN) AF: 0.643 AC: 6792 AN: 10556

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45808 AN: 67968

Other (OTH) AF: 0.684 AC: 1445 AN: 2112

Alfa AF: 0.689 Hom.: 70097

Bravo AF: 0.718

Asia WGS AF: 0.746 AC: 2594 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.27
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: rs6480245; hg19: chr10-68746991;