rs6013029
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030877.5(CTNNBL1):c.750+3134G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,160 control chromosomes in the GnomAD database, including 1,700 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 0.11 ( 1700 hom., cov: 32)
Consequence
CTNNBL1
NM_030877.5 intron
NM_030877.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.154
Genes affected
CTNNBL1 (HGNC:15879): (catenin beta like 1) The protein encoded by this gene is a component of the pre-mRNA-processing factor 19-cell division cycle 5-like (PRP19-CDC5L) protein complex, which activates pre-mRNA splicing and is an integral part of the spliceosome. The encoded protein is also a nuclear localization sequence binding protein, and binds to activation-induced deaminase and is important for antibody diversification. This gene may also be associated with the development of obesity. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been defined on the X chromosome. [provided by RefSeq, Jul 2013]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTNNBL1 | NM_030877.5 | c.750+3134G>T | intron_variant | ENST00000361383.11 | |||
CTNNBL1 | NM_001281495.2 | c.669+3134G>T | intron_variant | ||||
CTNNBL1 | XM_011528917.3 | c.420+3134G>T | intron_variant | ||||
CTNNBL1 | XM_024451947.2 | c.669+3134G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTNNBL1 | ENST00000361383.11 | c.750+3134G>T | intron_variant | 1 | NM_030877.5 | P1 | |||
CTNNBL1 | ENST00000373473.5 | c.189+3134G>T | intron_variant | 1 | |||||
CTNNBL1 | ENST00000628103.2 | c.669+3134G>T | intron_variant | 2 | |||||
CTNNBL1 | ENST00000473857.5 | n.1834+3134G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.114 AC: 17282AN: 152042Hom.: 1693 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.114 AC: 17319AN: 152160Hom.: 1700 Cov.: 32 AF XY: 0.111 AC XY: 8284AN XY: 74408
GnomAD4 genome
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32
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74408
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143
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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