10-66204615-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.134
Variant links:
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]

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ACMG classification

Classification made for transcript

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
CTNNA3NM_013266.4 linkc.1884+75855C>A intron_variant Intron 13 of 17 ENST00000433211.7 NP_037398.2 Q9UI47-1A8K141

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CTNNA3ENST00000433211.7 linkc.1884+75855C>A intron_variant Intron 13 of 17 1 NM_013266.4 ENSP00000389714.1 Q9UI47-1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1471384; hg19: chr10-67964373; API