20-37804886-T-C

Position:

• chr20-37804886-T-C

Variant summary

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

The NM_030877.5(CTNNBL1):​c.1213+1838T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,170 control chromosomes in the GnomAD database, including 3,915 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 0.20 (3915 hom., cov: 33)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.52

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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNBL1	NM_030877.5	c.1213+1838T>C		intron_variant		ENST00000361383.11
CTNNBL1	NM_001281495.2	c.1132+1838T>C		intron_variant
CTNNBL1	XM_011528917.3	c.883+1838T>C		intron_variant
CTNNBL1	XM_024451947.2	c.1132+1838T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.1213+1838T>C		intron_variant		1	NM_030877.5	P1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30761 AN: 152052 Hom.: 3912 Cov.: 33

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.202 AC: 30778 AN: 152170 Hom.: 3915 Cov.: 33 AF XY: 0.207 AC XY: 15421 AN XY: 74392

Gnomad4 AFR AF: 0.0527

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.207

Alfa AF: 0.223 Hom.: 1095

Bravo AF: 0.199

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	10
DANN	Benign	0.46

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: rs2281148; hg19: chr20-36433288;