20-37780962-G-A

Variant summary

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

The NM_030877.5(CTNNBL1):​c.1031+1627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,096 control chromosomes in the GnomAD database, including 55,654 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 0.85 ( 55654 hom., cov: 31)

Consequence

CTNNBL1
NM_030877.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.606
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTNNBL1NM_030877.5 linkuse as main transcriptc.1031+1627G>A intron_variant ENST00000361383.11
CTNNBL1NM_001281495.2 linkuse as main transcriptc.950+1627G>A intron_variant
CTNNBL1XM_011528917.3 linkuse as main transcriptc.701+1627G>A intron_variant
CTNNBL1XM_024451947.2 linkuse as main transcriptc.950+1627G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTNNBL1ENST00000361383.11 linkuse as main transcriptc.1031+1627G>A intron_variant 1 NM_030877.5 P1Q8WYA6-1

Frequencies

GnomAD3 genomes
AF:
0.852
AC:
129451
AN:
151978
Hom.:
55587
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.961
Gnomad AMI
AF:
0.886
Gnomad AMR
AF:
0.882
Gnomad ASJ
AF:
0.882
Gnomad EAS
AF:
0.864
Gnomad SAS
AF:
0.866
Gnomad FIN
AF:
0.732
Gnomad MID
AF:
0.892
Gnomad NFE
AF:
0.792
Gnomad OTH
AF:
0.865
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.852
AC:
129576
AN:
152096
Hom.:
55654
Cov.:
31
AF XY:
0.850
AC XY:
63213
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.961
Gnomad4 AMR
AF:
0.882
Gnomad4 ASJ
AF:
0.882
Gnomad4 EAS
AF:
0.864
Gnomad4 SAS
AF:
0.864
Gnomad4 FIN
AF:
0.732
Gnomad4 NFE
AF:
0.792
Gnomad4 OTH
AF:
0.866
Alfa
AF:
0.820
Hom.:
12904
Bravo
AF:
0.867
Asia WGS
AF:
0.886
AC:
3080
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
0.53
DANN
Benign
0.53

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: rs238303; hg19: chr20-36409364; API