rs16986921

Positions:

• chr20-37754119-C-T

Variant summary

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

The NM_030877.5(CTNNBL1):​c.467-3440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,062 control chromosomes in the GnomAD database, including 1,666 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 0.11 (1666 hom., cov: 32)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

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]

LOC124904895 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNBL1	NM_030877.5	c.467-3440C>T		intron_variant		ENST00000361383.11	NP_110517.2
LOC124904895	XR_007067575.1	n.6368C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.467-3440C>T		intron_variant		1	NM_030877.5	ENSP00000355050	P1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17122 AN: 151944 Hom.: 1659 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0554

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.113 AC: 17160 AN: 152062 Hom.: 1666 Cov.: 32 AF XY: 0.110 AC XY: 8200 AN XY: 74374

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.0100

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.0675

Gnomad4 NFE AF: 0.0554

Gnomad4 OTH AF: 0.110

Alfa AF: 0.106 Hom.: 307

Bravo AF: 0.120

Asia WGS AF: 0.0420 AC: 144 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	1.9
DANN	Benign	0.18

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: rs16986921; hg19: chr20-36382521;