rs9883073

Variant names:

• chr3-41243045-C-A
• rs9883073
• ENST00000471014.2:n.*12+3691C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-41243045-C-A
• chr3-41243045-C-T

Variant summary

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

The ENST00000471014.2(CTNNB1):​n.*12+3691C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,936 control chromosomes in the GnomAD database, including 11,813 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 0.39 (11813 hom., cov: 32)
• Consequence: CTNNB1 ENST00000471014.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

CTNNB1 (HGNC:2514): (catenin beta 1) The protein encoded by this gene is part of a complex of proteins that constitute adherens junctions (AJs). AJs are necessary for the creation and maintenance of epithelial cell layers by regulating cell growth and adhesion between cells. The encoded protein also anchors the actin cytoskeleton and may be responsible for transmitting the contact inhibition signal that causes cells to stop dividing once the epithelial sheet is complete. Finally, this protein binds to the product of the APC gene, which is mutated in adenomatous polyposis of the colon. Mutations in this gene are a cause of colorectal cancer (CRC), pilomatrixoma (PTR), medulloblastoma (MDB), and ovarian cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTNNB1	ENST00000471014.2	n.*12+3691C>A		intron_variant	Intron 4 of 5	3		ENSP00000495552.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58521 AN: 151818 Hom.: 11811 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.385 AC: 58539 AN: 151936 Hom.: 11813 Cov.: 32 AF XY: 0.382 AC XY: 28391 AN XY: 74262

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.378

Alfa AF: 0.432 Hom.: 28980

Bravo AF: 0.373

Asia WGS AF: 0.358 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9883073; hg19: chr3-41284536;