10-66204615-G-T

Variant names:

• chr10-66204615-G-T
• rs1471384
• NM_013266.4:c.1884+75855C>A

Variant summary

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

The NM_013266.4(CTNNA3):​c.1884+75855C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,118 control chromosomes in the GnomAD database, including 52,030 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 0.83 (52030 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTNNA3	NM_013266.4	c.1884+75855C>A		intron_variant	Intron 13 of 17	ENST00000433211.7	NP_037398.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTNNA3	ENST00000433211.7	c.1884+75855C>A		intron_variant	Intron 13 of 17	1	NM_013266.4	ENSP00000389714.1

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125534 AN: 152000 Hom.: 51972 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.826 AC: 125656 AN: 152118 Hom.: 52030 Cov.: 32 AF XY: 0.829 AC XY: 61650 AN XY: 74362

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.823

Alfa AF: 0.815 Hom.: 33445

Bravo AF: 0.830

Asia WGS AF: 0.865 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
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: rs1471384; hg19: chr10-67964373;