rs1344089

Variant summary

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

The NM_013266.4(CTNNA3):​c.1048-99091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,894 control chromosomes in the GnomAD database, including 14,310 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 0.43 ( 14310 hom., cov: 32)

Consequence

CTNNA3
NM_013266.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTNNA3NM_013266.4 linkuse as main transcriptc.1048-99091C>T intron_variant ENST00000433211.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTNNA3ENST00000433211.7 linkuse as main transcriptc.1048-99091C>T intron_variant 1 NM_013266.4 P1Q9UI47-1

Frequencies

GnomAD3 genomes
AF:
0.430
AC:
65205
AN:
151776
Hom.:
14299
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.426
Gnomad AMI
AF:
0.423
Gnomad AMR
AF:
0.376
Gnomad ASJ
AF:
0.412
Gnomad EAS
AF:
0.155
Gnomad SAS
AF:
0.354
Gnomad FIN
AF:
0.478
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.464
Gnomad OTH
AF:
0.418
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.430
AC:
65253
AN:
151894
Hom.:
14310
Cov.:
32
AF XY:
0.428
AC XY:
31733
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.426
Gnomad4 AMR
AF:
0.376
Gnomad4 ASJ
AF:
0.412
Gnomad4 EAS
AF:
0.155
Gnomad4 SAS
AF:
0.354
Gnomad4 FIN
AF:
0.478
Gnomad4 NFE
AF:
0.464
Gnomad4 OTH
AF:
0.417
Alfa
AF:
0.314
Hom.:
821
Bravo
AF:
0.417
Asia WGS
AF:
0.291
AC:
1006
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.23
DANN
Benign
0.72

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: rs1344089; hg19: chr10-68634373; API