chr20-37711234-T-C

Variant names:

• chr20-37711234-T-C
• rs6067377
• NM_030877.5:c.30+17082T>C

Variant summary

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

The NM_030877.5(CTNNBL1):​c.30+17082T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,896 control chromosomes in the GnomAD database, including 20,338 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 0.49 (20338 hom., cov: 31)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTNNBL1	NM_030877.5	c.30+17082T>C		intron_variant	Intron 1 of 15	ENST00000361383.11	NP_110517.2
CTNNBL1	NM_001281495.2	c.-152-16068T>C		intron_variant	Intron 1 of 16		NP_001268424.1
CTNNBL1	XM_024451947.2	c.-52+16201T>C		intron_variant	Intron 2 of 16		XP_024307715.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.30+17082T>C		intron_variant	Intron 1 of 15	1	NM_030877.5	ENSP00000355050.6
CTNNBL1	ENST00000628103.2	c.-152-16068T>C		intron_variant	Intron 1 of 16	2		ENSP00000487198.1
CTNNBL1	ENST00000447935.3	c.-52+16201T>C		intron_variant	Intron 2 of 6	5		ENSP00000394464.1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74057 AN: 151778 Hom.: 20301 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.488 AC: 74145 AN: 151896 Hom.: 20338 Cov.: 31 AF XY: 0.485 AC XY: 35970 AN XY: 74236

African (AFR) AF: 0.756 AC: 31282 AN: 41402

American (AMR) AF: 0.431 AC: 6582 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5162

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4810

European-Finnish (FIN) AF: 0.483 AC: 5088 AN: 10544

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26396 AN: 67928

Other (OTH) AF: 0.438 AC: 922 AN: 2106

Alfa AF: 0.409 Hom.: 6956

Bravo AF: 0.498

Asia WGS AF: 0.266 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.52
PhyloP100		0.12
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: rs6067377; hg19: chr20-36339636;