rs6067923

Variant names:

• chr20-37861662-G-A
• rs6067923
• NM_030877.5:c.1603+1318G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-37861662-G-A
• chr20-37861662-G-C
• chr20-37861662-G-T

Variant summary

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

The NM_030877.5(CTNNBL1):​c.1603+1318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,064 control chromosomes in the GnomAD database, including 11,182 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 0.38 (11182 hom., cov: 33)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTNNBL1	NM_030877.5	c.1603+1318G>A		intron_variant	Intron 15 of 15	ENST00000361383.11	NP_110517.2
CTNNBL1	NM_001281495.2	c.1522+1318G>A		intron_variant	Intron 16 of 16		NP_001268424.1
CTNNBL1	XM_024451947.2	c.1522+1318G>A		intron_variant	Intron 16 of 16		XP_024307715.1
CTNNBL1	XM_011528917.3	c.1273+1318G>A		intron_variant	Intron 13 of 13		XP_011527219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.1603+1318G>A		intron_variant	Intron 15 of 15	1	NM_030877.5	ENSP00000355050.6
CTNNBL1	ENST00000628103.2	c.1522+1318G>A		intron_variant	Intron 16 of 16	2		ENSP00000487198.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57453 AN: 151946 Hom.: 11172 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.378 AC: 57501 AN: 152064 Hom.: 11182 Cov.: 33 AF XY: 0.383 AC XY: 28475 AN XY: 74310

African (AFR) AF: 0.359 AC: 14885 AN: 41480

American (AMR) AF: 0.494 AC: 7549 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2344 AN: 5162

South Asian (SAS) AF: 0.405 AC: 1949 AN: 4816

European-Finnish (FIN) AF: 0.408 AC: 4302 AN: 10556

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24020 AN: 67980

Other (OTH) AF: 0.377 AC: 797 AN: 2112

Alfa AF: 0.364 Hom.: 28925

Bravo AF: 0.387

Asia WGS AF: 0.404 AC: 1402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		0.025
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: rs6067923; hg19: chr20-36490064;