rs2306402

Variant summary

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

The NM_013266.4(CTNNA3):​c.1047+4590G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,992 control chromosomes in the GnomAD database, including 14,580 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 0.37 ( 14580 hom., cov: 32)

Consequence

CTNNA3
NM_013266.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.339
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTNNA3NM_013266.4 linkuse as main transcriptc.1047+4590G>A intron_variant ENST00000433211.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTNNA3ENST00000433211.7 linkuse as main transcriptc.1047+4590G>A intron_variant 1 NM_013266.4 P1Q9UI47-1

Frequencies

GnomAD3 genomes
AF:
0.365
AC:
55506
AN:
151874
Hom.:
14537
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.748
Gnomad AMI
AF:
0.171
Gnomad AMR
AF:
0.247
Gnomad ASJ
AF:
0.197
Gnomad EAS
AF:
0.121
Gnomad SAS
AF:
0.385
Gnomad FIN
AF:
0.255
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.207
Gnomad OTH
AF:
0.330
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.366
AC:
55600
AN:
151992
Hom.:
14580
Cov.:
32
AF XY:
0.366
AC XY:
27197
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.748
Gnomad4 AMR
AF:
0.247
Gnomad4 ASJ
AF:
0.197
Gnomad4 EAS
AF:
0.122
Gnomad4 SAS
AF:
0.385
Gnomad4 FIN
AF:
0.255
Gnomad4 NFE
AF:
0.207
Gnomad4 OTH
AF:
0.326
Alfa
AF:
0.313
Hom.:
1706
Bravo
AF:
0.378
Asia WGS
AF:
0.265
AC:
923
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.8
DANN
Benign
0.60

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: rs2306402; hg19: chr10-68935485; API