rs1798802

Variant summary

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

The ENST00000349496.11(CTNNB1):​c.-48-3533A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 149,700 control chromosomes in the GnomAD database, including 15,096 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 ( 15096 hom., cov: 26)
Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

CTNNB1
ENST00000349496.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.396
Variant links:
Genes affected
CTNNB1 (HGNC:2514): (catenin beta 1) The protein encoded by this gene is part of a complex of proteins that constitute adherens junctions (AJs). AJs are necessary for the creation and maintenance of epithelial cell layers by regulating cell growth and adhesion between cells. The encoded protein also anchors the actin cytoskeleton and may be responsible for transmitting the contact inhibition signal that causes cells to stop dividing once the epithelial sheet is complete. Finally, this protein binds to the product of the APC gene, which is mutated in adenomatous polyposis of the colon. Mutations in this gene are a cause of colorectal cancer (CRC), pilomatrixoma (PTR), medulloblastoma (MDB), and ovarian cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CTNNB1NM_001904.4 linkuse as main transcriptc.-48-3533A>G intron_variant ENST00000349496.11 NP_001895.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CTNNB1ENST00000349496.11 linkuse as main transcriptc.-48-3533A>G intron_variant 1 NM_001904.4 ENSP00000344456 P4

Frequencies

GnomAD3 genomes
AF:
0.433
AC:
64783
AN:
149582
Hom.:
15094
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.263
Gnomad AMI
AF:
0.445
Gnomad AMR
AF:
0.402
Gnomad ASJ
AF:
0.587
Gnomad EAS
AF:
0.694
Gnomad SAS
AF:
0.536
Gnomad FIN
AF:
0.448
Gnomad MID
AF:
0.542
Gnomad NFE
AF:
0.503
Gnomad OTH
AF:
0.466
GnomAD4 exome
AF:
0.500
AC:
1
AN:
2
Hom.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.433
AC:
64797
AN:
149698
Hom.:
15096
Cov.:
26
AF XY:
0.435
AC XY:
31687
AN XY:
72912
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.402
Gnomad4 ASJ
AF:
0.587
Gnomad4 EAS
AF:
0.694
Gnomad4 SAS
AF:
0.538
Gnomad4 FIN
AF:
0.448
Gnomad4 NFE
AF:
0.503
Gnomad4 OTH
AF:
0.468
Alfa
AF:
0.489
Hom.:
8798
Bravo
AF:
0.414
Asia WGS
AF:
0.545
AC:
1890
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
7.4
DANN
Benign
0.75

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: rs1798802; hg19: chr3-41261979; API