chr1-9851233-A-G

Variant names:

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

Variant summary

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

The NM_020248.3(CTNNBIP1):​c.188-457T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,108 control chromosomes in the GnomAD database, including 6,332 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 0.27 (6332 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNNBIP1	NM_020248.3	MANE Select	c.188-457T>C		intron	N/A	NP_064633.1
	CTNNBIP1	NM_001012329.2		c.188-457T>C		intron	N/A	NP_001012329.1

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40915 AN: 151990 Hom.: 6318 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.269 AC: 40977 AN: 152108 Hom.: 6332 Cov.: 33 AF XY: 0.276 AC XY: 20524 AN XY: 74364

African (AFR) AF: 0.281 AC: 11648 AN: 41460

American (AMR) AF: 0.273 AC: 4185 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3472

East Asian (EAS) AF: 0.747 AC: 3867 AN: 5180

South Asian (SAS) AF: 0.373 AC: 1800 AN: 4820

European-Finnish (FIN) AF: 0.267 AC: 2820 AN: 10576

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15070 AN: 67984

Other (OTH) AF: 0.242 AC: 512 AN: 2114

Alfa AF: 0.242 Hom.: 13875

Bravo AF: 0.272

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.85
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: rs2379107; hg19: chr1-9911291; COSMIC: COSV65962196; COSMIC: COSV65962196;