chr20-37857818-G-C

Position:

• chr20-37857818-G-C

Variant summary

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

The NM_030877.5(CTNNBL1):​c.1393-2081G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,158 control chromosomes in the GnomAD database, including 39,323 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 0.72 (39323 hom., cov: 32)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

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 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNBL1	NM_030877.5	c.1393-2081G>C		intron_variant		ENST00000361383.11	NP_110517.2
CTNNBL1	NM_001281495.2	c.1312-2081G>C		intron_variant			NP_001268424.1
CTNNBL1	XM_024451947.2	c.1312-2081G>C		intron_variant			XP_024307715.1
CTNNBL1	XM_011528917.3	c.1063-2081G>C		intron_variant			XP_011527219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.1393-2081G>C		intron_variant		1	NM_030877.5	ENSP00000355050.6
CTNNBL1	ENST00000628103.2	c.1312-2081G>C		intron_variant		2		ENSP00000487198.1

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108969 AN: 152040 Hom.: 39278 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.741

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.717 AC: 109070 AN: 152158 Hom.: 39323 Cov.: 32 AF XY: 0.715 AC XY: 53204 AN XY: 74376

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.744

Alfa AF: 0.544 Hom.: 905

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.51

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: rs4811233; hg19: chr20-36486220;