rs7900716

Variant names:

• chr10-67017255-T-C
• rs7900716
• NM_013266.4:c.1047+163062A>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+163062A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,216 control chromosomes in the GnomAD database, including 1,174 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 0.11 (1174 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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+163062A>G		intron	N/A	NP_037398.2	Q9UI47-1
	LRRTM3	NM_178011.5	MANE Select	c.1537-80332T>C		intron	N/A	NP_821079.3
	CTNNA3	NM_001127384.3		c.1047+163062A>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+163062A>G		intron	N/A	ENSP00000389714.1	Q9UI47-1
	LRRTM3	ENST00000361320.5	TSL:1 MANE Select	c.1537-80332T>C		intron	N/A	ENSP00000355187.3	Q86VH5-1
	CTNNA3	ENST00000682758.1		c.1047+163062A>G		intron	N/A	ENSP00000508047.1	Q9UI47-1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16951 AN: 152098 Hom.: 1171 Cov.: 32

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00730

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.111 AC: 16961 AN: 152216 Hom.: 1174 Cov.: 32 AF XY: 0.114 AC XY: 8463 AN XY: 74426

African (AFR) AF: 0.0542 AC: 2250 AN: 41548

American (AMR) AF: 0.0987 AC: 1509 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.00732 AC: 38 AN: 5192

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4814

European-Finnish (FIN) AF: 0.136 AC: 1443 AN: 10582

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9531 AN: 67998

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.133 Hom.: 2775

Bravo AF: 0.101

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		-0.12
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: rs7900716; hg19: chr10-68777013;