rs1925621

Variant names:

• chr10-67009839-T-A
• rs1925621
• NM_013266.4:c.1047+170478A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-67009839-T-A
• chr10-67009839-T-C

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+170478A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,972 control chromosomes in the GnomAD database, including 21,977 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 0.53 (21977 hom., cov: 32)
• Consequence: CTNNA3 NM_013266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 1 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=-0.91).
• 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 rank	MANE	Protein	UniProt
CTNNA3	NM_013266.4	c.1047+170478A>T		intron_variant	Intron 7 of 17	ENST00000433211.7	NP_037398.2
LRRTM3	NM_178011.5	c.1536+81387T>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+170478A>T		intron_variant	Intron 7 of 17	1	NM_013266.4	ENSP00000389714.1
LRRTM3	ENST00000361320.5	c.1536+81387T>A		intron_variant	Intron 2 of 2	1	NM_178011.5	ENSP00000355187.3

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80390 AN: 151852 Hom.: 21975 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.529 AC: 80419 AN: 151972 Hom.: 21977 Cov.: 32 AF XY: 0.531 AC XY: 39452 AN XY: 74290

African (AFR) AF: 0.458 AC: 18983 AN: 41460

American (AMR) AF: 0.483 AC: 7376 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2357 AN: 3466

East Asian (EAS) AF: 0.228 AC: 1178 AN: 5166

South Asian (SAS) AF: 0.597 AC: 2876 AN: 4816

European-Finnish (FIN) AF: 0.621 AC: 6551 AN: 10552

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39156 AN: 67938

Other (OTH) AF: 0.571 AC: 1205 AN: 2112

Alfa AF: 0.536 Hom.: 2751

Bravo AF: 0.515

Asia WGS AF: 0.432 AC: 1503 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.76
PhyloP100		0.39
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1925621; hg19: chr10-68769597;