1-9851233-A-T

Variant names:

• chr1-9851233-A-T
• rs2379107
• NM_020248.3:c.188-457T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020248.3(CTNNBIP1):​c.188-457T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: CTNNBIP1 NM_020248.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 6 publications found

Genes affected

CTNNBIP1 (HGNC:16913): (catenin beta interacting protein 1) The protein encoded by this gene binds CTNNB1 and prevents interaction between CTNNB1 and TCF family members. The encoded protein is a negative regulator of the Wnt signaling pathway. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

LOC105376717 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020248.3. 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
	CTNNBIP1	NM_020248.3	MANE Select	c.188-457T>A		intron	N/A	NP_064633.1	Q9NSA3
	CTNNBIP1	NM_001012329.2		c.188-457T>A		intron	N/A	NP_001012329.1	Q9NSA3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNNBIP1	ENST00000377263.6	TSL:1 MANE Select	c.188-457T>A		intron	N/A	ENSP00000366474.1	Q9NSA3
	CTNNBIP1	ENST00000400904.7	TSL:1	c.188-457T>A		intron	N/A	ENSP00000383696.3	Q9NSA3
	CTNNBIP1	ENST00000377256.1	TSL:5	c.188-457T>A		intron	N/A	ENSP00000366466.1	Q9NSA3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.85
PhyloP100		-0.85

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: rs2379107; hg19: chr1-9911291;