rs935073
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_020248.3 intron
Scores
2
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]
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ACMG classification
Classification made for transcript
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: 45664AN: 152048Hom.: 9316 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.301 AC: 45751AN: 152166Hom.: 9347 Cov.: 32 AF XY: 0.298 AC XY: 22179AN XY: 74388
GnomAD4 genome
?
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32
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22179
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74388
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1261
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at