rs1372106

chr1-9904650-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.-144+5445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,124 control chromosomes in the GnomAD database, including 1,838 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 0.15 (1838 hom., cov: 32)
• Consequence: CTNNBIP1 NM_020248.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNBIP1	NM_020248.3	c.-144+5445T>C		intron_variant		ENST00000377263.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNBIP1	ENST00000377263.6	c.-144+5445T>C		intron_variant		1	NM_020248.3	P1
CTNNBIP1	ENST00000400904.7	c.-110+5445T>C		intron_variant		1		P1
	ENST00000648956.1	n.484+245A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23007 AN: 152006 Hom.: 1832 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.151 AC: 23043 AN: 152124 Hom.: 1838 Cov.: 32 AF XY: 0.149 AC XY: 11103 AN XY: 74368

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0535

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.146

Alfa AF: 0.162 Hom.: 520

Bravo AF: 0.143

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.3
Dann	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1372106; hg19: chr1-9964708;