rs6126098

Positions:

• chr20-37762430-G-A

Variant summary

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

The NM_030877.5(CTNNBL1):​c.565-2767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,890 control chromosomes in the GnomAD database, including 7,823 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 0.30 (7823 hom., cov: 32)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

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=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNBL1	NM_030877.5	c.565-2767G>A		intron_variant		ENST00000361383.11
CTNNBL1	NM_001281495.2	c.484-2767G>A		intron_variant
CTNNBL1	XM_011528917.3	c.235-2767G>A		intron_variant
CTNNBL1	XM_024451947.2	c.484-2767G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.565-2767G>A		intron_variant		1	NM_030877.5	P1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45749 AN: 151772 Hom.: 7825 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.301 AC: 45747 AN: 151890 Hom.: 7823 Cov.: 32 AF XY: 0.301 AC XY: 22342 AN XY: 74230

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.355

Alfa AF: 0.345 Hom.: 2285

Bravo AF: 0.293

Asia WGS AF: 0.421 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	14
DANN	Benign	0.61

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: rs6126098; hg19: chr20-36390832;