Variant rs45500793 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_030877.5(CTNNBL1):c.1393-16G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00719 in 1,612,994 control chromosomes in the GnomAD database, including 62 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 0.0047 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0075 ( 61 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 -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BS2

High Homozygotes in GnomAdExome4 at 61 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CTNNBL1	NM_030877.5 link	c.1393-16G>A	intron_variant	ENST00000361383.11	NP_110517.2	Q8WYA6-1
CTNNBL1	NM_001281495.2 link	c.1312-16G>A	intron_variant		NP_001268424.1	Q8WYA6-4
CTNNBL1	XM_024451947.2 link	c.1312-16G>A	intron_variant		XP_024307715.1
CTNNBL1	XM_011528917.3 link	c.1063-16G>A	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>A		intron_variant		1	NM_030877.5	ENSP00000355050.6		Q8WYA6-1
CTNNBL1	ENST00000628103.2 link	c.1312-16G>A		intron_variant		2		ENSP00000487198.1		Q8WYA6-4

Frequencies

GnomAD3 genomes

AF:

0.00467

AC:

710

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00445

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00254

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00797

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00424

AC:

1062

AN:

250252

Hom.:

AF XY:

0.00426

AC XY:

576

AN XY:

135274

show subpopulations

Gnomad AFR exome

AF:

0.00129

Gnomad AMR exome

AF:

0.00311

Gnomad ASJ exome

AF:

0.00220

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000361

Gnomad FIN exome

AF:

0.00191

Gnomad NFE exome

AF:

0.00737

Gnomad OTH exome

AF:

0.00426

GnomAD4 exome

AF:

0.00746

AC:

10895

AN:

1460746

Hom.:

Cov.:

AF XY:

0.00714

AC XY:

5189

AN XY:

726592

show subpopulations

Gnomad4 AFR exome

AF:

0.00131

Gnomad4 AMR exome

AF:

0.00284

Gnomad4 ASJ exome

AF:

0.00242

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000372

Gnomad4 FIN exome

AF:

0.00204

Gnomad4 NFE exome

AF:

0.00918

Gnomad4 OTH exome

AF:

0.00515

GnomAD4 genome

AF:

0.00466

AC:

710

AN:

152248

Hom.:

Cov.:

AF XY:

0.00434

AC XY:

323

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00123

Gnomad4 AMR

AF:

0.00445

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00254

Gnomad4 NFE

AF:

0.00797

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00242

Hom.:

Bravo

AF:

0.00470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

9.9

DANN

Benign

0.74

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