rs1925583

chr10-66920186-A-C

Variant summary

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

The NM_013266.4(CTNNA3):c.1048-144662T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,042 control chromosomes in the GnomAD database, including 12,964 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 0.41 (12964 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.946

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]

LOC101928961 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA3	NM_013266.4	c.1048-144662T>G		intron_variant		ENST00000433211.7
LOC101928961	NR_111911.1	n.2718-9693T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA3	ENST00000433211.7	c.1048-144662T>G		intron_variant		1	NM_013266.4	P1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61832 AN: 151924 Hom.: 12956 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.407 AC: 61878 AN: 152042 Hom.: 12964 Cov.: 32 AF XY: 0.406 AC XY: 30151 AN XY: 74324

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.408

Alfa AF: 0.431 Hom.: 2449

Bravo AF: 0.394

Asia WGS AF: 0.301 AC: 1045 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	7.9
Dann	Benign	0.73

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: rs1925583; hg19: chr10-68679944;