chr20-37745733-A-G

Variant names:

• chr20-37745733-A-G
• rs6067491
• NM_030877.5:c.327-735A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030877.5(CTNNBL1):​c.327-735A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,028 control chromosomes in the GnomAD database, including 8,277 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 0.33 (8277 hom., cov: 32)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 12 publications found

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 Gene-Disease associations (from GenCC):

• common variable immunodeficiency

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen
• immunodeficiency 99 with hypogammaglobulinemia and autoimmune cytopenias

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTNNBL1	NM_030877.5	c.327-735A>G		intron_variant	Intron 3 of 15	ENST00000361383.11	NP_110517.2
CTNNBL1	NM_001281495.2	c.246-735A>G		intron_variant	Intron 4 of 16		NP_001268424.1
CTNNBL1	XM_024451947.2	c.246-735A>G		intron_variant	Intron 4 of 16		XP_024307715.1
CTNNBL1	XM_011528917.3	c.-4-735A>G		intron_variant	Intron 1 of 13		XP_011527219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.327-735A>G		intron_variant	Intron 3 of 15	1	NM_030877.5	ENSP00000355050.6
CTNNBL1	ENST00000628103.2	c.246-735A>G		intron_variant	Intron 4 of 16	2		ENSP00000487198.1
CTNNBL1	ENST00000373473.5	c.-177-735A>G		intron_variant	Intron 1 of 12	1		ENSP00000362572.1
CTNNBL1	ENST00000447935.3	c.246-735A>G		intron_variant	Intron 4 of 6	5		ENSP00000394464.1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49787 AN: 151910 Hom.: 8267 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.328 AC: 49827 AN: 152028 Hom.: 8277 Cov.: 32 AF XY: 0.328 AC XY: 24385 AN XY: 74302

African (AFR) AF: 0.354 AC: 14670 AN: 41450

American (AMR) AF: 0.331 AC: 5052 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3468

East Asian (EAS) AF: 0.169 AC: 873 AN: 5170

South Asian (SAS) AF: 0.272 AC: 1310 AN: 4814

European-Finnish (FIN) AF: 0.406 AC: 4287 AN: 10562

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21992 AN: 67970

Other (OTH) AF: 0.289 AC: 610 AN: 2108

Alfa AF: 0.321 Hom.: 34545

Bravo AF: 0.325

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	14
DANN	Benign	0.61
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6067491; hg19: chr20-36374135;