Variant 20-37859883-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_030877.5(CTNNBL1):c.1393-16G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 1,612,982 control chromosomes in the GnomAD database, including 240 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 0.011 ( 10 hom., cov: 32)

Exomes 𝑓: 0.016 ( 230 hom. )

Consequence

CTNNBL1
NM_030877.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65

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]

CTNNBL1 links:

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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=-0.8).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0109 (1665/152252) while in subpopulation NFE AF= 0.017 (1153/68016). AF 95% confidence interval is 0.0161. There are 10 homozygotes in gnomad4. There are 769 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CTNNBL1	NM_030877.5 link	c.1393-16G>T	intron_variant	ENST00000361383.11	NP_110517.2	Q8WYA6-1
CTNNBL1	NM_001281495.2 link	c.1312-16G>T	intron_variant		NP_001268424.1	Q8WYA6-4
CTNNBL1	XM_024451947.2 link	c.1312-16G>T	intron_variant		XP_024307715.1
CTNNBL1	XM_011528917.3 link	c.1063-16G>T	intron_variant		XP_011527219.1	Q8WYA6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNNBL1	ENST00000361383.11 link	c.1393-16G>T		intron_variant		1	NM_030877.5	ENSP00000355050.6		Q8WYA6-1
CTNNBL1	ENST00000628103.2 link	c.1312-16G>T		intron_variant		2		ENSP00000487198.1		Q8WYA6-4

Frequencies

GnomAD3 genomes

AF:

0.0109

AC:

1664

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00345

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0164

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.00556

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0169

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.00963

AC:

2410

AN:

250252

Hom.:

AF XY:

0.00954

AC XY:

1290

AN XY:

135274

show subpopulations

Gnomad AFR exome

AF:

0.00376

Gnomad AMR exome

AF:

0.0102

Gnomad ASJ exome

AF:

0.00479

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00240

Gnomad FIN exome

AF:

0.00465

Gnomad NFE exome

AF:

0.0150

Gnomad OTH exome

AF:

0.0121

GnomAD4 exome

AF:

0.0160

AC:

23310

AN:

1460730

Hom.:

230

Cov.:

AF XY:

0.0154

AC XY:

11196

AN XY:

726580

show subpopulations

Gnomad4 AFR exome

AF:

0.00296

Gnomad4 AMR exome

AF:

0.0101

Gnomad4 ASJ exome

AF:

0.00499

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00233

Gnomad4 FIN exome

AF:

0.00506

Gnomad4 NFE exome

AF:

0.0191

Gnomad4 OTH exome

AF:

0.0145

GnomAD4 genome

AF:

0.0109

AC:

1665

AN:

152252

Hom.:

Cov.:

AF XY:

0.0103

AC XY:

769

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00344

Gnomad4 AMR

AF:

0.0164

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00556

Gnomad4 NFE

AF:

0.0170

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.00466

Hom.:

Bravo

AF:

0.0116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.6

DANN

Benign

0.70

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over