rs4811144

chr20-37813412-C-Achr20-37813412-C-Gchr20-37813412-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

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]

ACMG classification

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
CTNNBL1	NM_030877.5	c.1213+10364C>A		intron_variant		ENST00000361383.11
CTNNBL1	NM_001281495.2	c.1132+10364C>A		intron_variant
CTNNBL1	XM_011528917.3	c.883+10364C>A		intron_variant
CTNNBL1	XM_024451947.2	c.1132+10364C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.1213+10364C>A		intron_variant		1	NM_030877.5	P1

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123493 AN: 152066 Hom.: 50197 Cov.: 32

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

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

Other links and lift over

dbSNP: rs4811144; hg19: chr20-36441814;