chr1-9863683-A-G

Position:

• chr1-9863683-A-G

Variant summary

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

The NM_020248.3(CTNNBIP1):​c.187+7504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,166 control chromosomes in the GnomAD database, including 9,347 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 0.30 (9347 hom., cov: 32)
• Consequence: CTNNBIP1 NM_020248.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.40

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNBIP1	NM_020248.3	c.187+7504T>C		intron_variant		ENST00000377263.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNBIP1	ENST00000377263.6	c.187+7504T>C		intron_variant		1	NM_020248.3	P1
CTNNBIP1	ENST00000400904.7	c.187+7504T>C		intron_variant		1		P1
CTNNBIP1	ENST00000377256.1	c.187+7504T>C		intron_variant		5		P1
CTNNBIP1	ENST00000377258.5	c.187+7504T>C		intron_variant		3		P1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45664 AN: 152048 Hom.: 9316 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.301 AC: 45751 AN: 152166 Hom.: 9347 Cov.: 32 AF XY: 0.298 AC XY: 22179 AN XY: 74388

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.258

Alfa AF: 0.274 Hom.: 1526

Bravo AF: 0.309

Asia WGS AF: 0.362 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.037
DANN	Benign	0.26

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: rs935073; hg19: chr1-9923741;