Variant chr20-37746669-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_030877.5(CTNNBL1):c.466+62T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 1,582,316 control chromosomes in the GnomAD database, including 697,335 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.95 ( 69421 hom., cov: 32)

Exomes 𝑓: 0.94 ( 627914 hom. )

Consequence

CTNNBL1
NM_030877.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00200

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 20-37746669-T-C is Benign according to our data. Variant chr20-37746669-T-C is described in ClinVar as [Benign]. Clinvar id is 2687972.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CTNNBL1	NM_030877.5 linkuse as main transcript	c.466+62T>C	intron_variant	ENST00000361383.11
CTNNBL1	NM_001281495.2 linkuse as main transcript	c.385+62T>C	intron_variant
CTNNBL1	XM_011528917.3 linkuse as main transcript	c.136+62T>C	intron_variant
CTNNBL1	XM_024451947.2 linkuse as main transcript	c.385+62T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
CTNNBL1	ENST00000361383.11 linkuse as main transcript	c.466+62T>C	intron_variant	1	NM_030877.5	P1	Q8WYA6-1
CTNNBL1	ENST00000373473.5 linkuse as main transcript	c.3+22T>C	intron_variant	1			Q8WYA6-2
CTNNBL1	ENST00000447935.3 linkuse as main transcript	c.385+62T>C	intron_variant	5
CTNNBL1	ENST00000628103.2 linkuse as main transcript	c.385+62T>C	intron_variant	2			Q8WYA6-4

Frequencies

GnomAD3 genomes

AF:

0.954

AC:

145228

AN:

152218

Hom.:

69361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.988

Gnomad AMI

AF:

0.889

Gnomad AMR

AF:

0.952

Gnomad ASJ

AF:

0.873

Gnomad EAS

AF:

0.975

Gnomad SAS

AF:

0.909

Gnomad FIN

AF:

0.982

Gnomad MID

AF:

0.813

Gnomad NFE

AF:

0.938

Gnomad OTH

AF:

0.934

GnomAD3 exomes

AF:

0.944

AC:

235875

AN:

249972

Hom.:

111483

AF XY:

0.938

AC XY:

126789

AN XY:

135188

show subpopulations

Gnomad AFR exome

AF:

0.989

Gnomad AMR exome

AF:

0.966

Gnomad ASJ exome

AF:

0.880

Gnomad EAS exome

AF:

0.979

Gnomad SAS exome

AF:

0.895

Gnomad FIN exome

AF:

0.979

Gnomad NFE exome

AF:

0.937

Gnomad OTH exome

AF:

0.929

GnomAD4 exome

AF:

0.937

AC:

1339389

AN:

1429980

Hom.:

627914

Cov.:

AF XY:

0.934

AC XY:

666683

AN XY:

713550

show subpopulations

Gnomad4 AFR exome

AF:

0.988

Gnomad4 AMR exome

AF:

0.965

Gnomad4 ASJ exome

AF:

0.880

Gnomad4 EAS exome

AF:

0.964

Gnomad4 SAS exome

AF:

0.896

Gnomad4 FIN exome

AF:

0.979

Gnomad4 NFE exome

AF:

0.936

Gnomad4 OTH exome

AF:

0.932

GnomAD4 genome

AF:

0.954

AC:

145347

AN:

152336

Hom.:

69421

Cov.:

AF XY:

0.955

AC XY:

71126

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.988

Gnomad4 AMR

AF:

0.952

Gnomad4 ASJ

AF:

0.873

Gnomad4 EAS

AF:

0.975

Gnomad4 SAS

AF:

0.909

Gnomad4 FIN

AF:

0.982

Gnomad4 NFE

AF:

0.938

Gnomad4 OTH

AF:

0.935

Alfa

AF:

0.938

Hom.:

20880

Bravo

AF:

0.954

Asia WGS

AF:

0.948

AC:

3294

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 100% of patients studied by a panel of primary immunodeficiencies. Number of patients: 95. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

8.2

DANN

Benign

0.62

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over