rs6067647

Variant names:

• chr20-37796949-A-G
• rs6067647
• NM_030877.5:c.1032-5918A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-37796949-A-G
• chr20-37796949-A-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.1032-5918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,558 control chromosomes in the GnomAD database, including 23,651 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 0.54 (23651 hom., cov: 30)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030877.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNNBL1	NM_030877.5	MANE Select	c.1032-5918A>G		intron	N/A	NP_110517.2
	CTNNBL1	NM_001281495.2		c.951-5918A>G		intron	N/A	NP_001268424.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNNBL1	ENST00000361383.11	TSL:1 MANE Select	c.1032-5918A>G		intron	N/A	ENSP00000355050.6
	CTNNBL1	ENST00000628103.2	TSL:2	c.951-5918A>G		intron	N/A	ENSP00000487198.1
	CTNNBL1	ENST00000373473.5	TSL:1	c.471-5918A>G		intron	N/A	ENSP00000362572.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81651 AN: 151440 Hom.: 23642 Cov.: 30

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.539 AC: 81681 AN: 151558 Hom.: 23651 Cov.: 30 AF XY: 0.544 AC XY: 40258 AN XY: 74044

African (AFR) AF: 0.307 AC: 12711 AN: 41388

American (AMR) AF: 0.580 AC: 8837 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2456 AN: 3460

East Asian (EAS) AF: 0.826 AC: 4248 AN: 5142

South Asian (SAS) AF: 0.695 AC: 3340 AN: 4804

European-Finnish (FIN) AF: 0.568 AC: 5953 AN: 10478

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42272 AN: 67752

Other (OTH) AF: 0.579 AC: 1218 AN: 2102

Alfa AF: 0.605 Hom.: 16263

Bravo AF: 0.529

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.99
DANN	Benign	0.31
PhyloP100		-0.60
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: rs6067647; hg19: chr20-36425351;