rs4811144

Variant summary

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

The NM_030877.5(CTNNBL1):​c.1213+10364C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,186 control chromosomes in the GnomAD database, including 50,250 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 0.81 ( 50250 hom., cov: 32)

Consequence

CTNNBL1
NM_030877.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.328
Variant links:
Genes affected
CTNNBL1 (HGNC:15879): (catenin beta like 1) The protein encoded by this gene is a component of the pre-mRNA-processing factor 19-cell division cycle 5-like (PRP19-CDC5L) protein complex, which activates pre-mRNA splicing and is an integral part of the spliceosome. The encoded protein is also a nuclear localization sequence binding protein, and binds to activation-induced deaminase and is important for antibody diversification. This gene may also be associated with the development of obesity. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been defined on the X chromosome. [provided by RefSeq, Jul 2013]

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=-0.97).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTNNBL1NM_030877.5 linkuse as main transcriptc.1213+10364C>A intron_variant ENST00000361383.11
CTNNBL1NM_001281495.2 linkuse as main transcriptc.1132+10364C>A intron_variant
CTNNBL1XM_011528917.3 linkuse as main transcriptc.883+10364C>A intron_variant
CTNNBL1XM_024451947.2 linkuse as main transcriptc.1132+10364C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTNNBL1ENST00000361383.11 linkuse as main transcriptc.1213+10364C>A intron_variant 1 NM_030877.5 P1Q8WYA6-1

Frequencies

GnomAD3 genomes
AF:
0.812
AC:
123493
AN:
152066
Hom.:
50197
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.813
Gnomad AMI
AF:
0.885
Gnomad AMR
AF:
0.871
Gnomad ASJ
AF:
0.882
Gnomad EAS
AF:
0.871
Gnomad SAS
AF:
0.864
Gnomad FIN
AF:
0.736
Gnomad MID
AF:
0.877
Gnomad NFE
AF:
0.796
Gnomad OTH
AF:
0.845
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.812
AC:
123604
AN:
152186
Hom.:
50250
Cov.:
32
AF XY:
0.812
AC XY:
60380
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.813
Gnomad4 AMR
AF:
0.872
Gnomad4 ASJ
AF:
0.882
Gnomad4 EAS
AF:
0.871
Gnomad4 SAS
AF:
0.862
Gnomad4 FIN
AF:
0.736
Gnomad4 NFE
AF:
0.796
Gnomad4 OTH
AF:
0.847
Alfa
AF:
0.801
Hom.:
10797
Bravo
AF:
0.822
Asia WGS
AF:
0.876
AC:
3043
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.32
DANN
Benign
0.28

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: rs4811144; hg19: chr20-36441814; API