chr11-8089993-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_177972.3(TUB):c.91-76T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 1,477,852 control chromosomes in the GnomAD database, including 330,398 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 0.64 ( 31299 hom., cov: 35)
Exomes 𝑓: 0.67 ( 299099 hom. )
Consequence
TUB
NM_177972.3 intron
NM_177972.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.609
Genes affected
TUB (HGNC:12406): (TUB bipartite transcription factor) This gene encodes a member of the Tubby family of bipartite transcription factors. The encoded protein may play a role in obesity and sensorineural degradation. The crystal structure has been determined for a similar protein in mouse, and it functions as a membrane-bound transcription regulator that translocates to the nucleus in response to phosphoinositide hydrolysis. Two transcript variants encoding distinct isoforms have been identified 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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUB | NM_177972.3 | c.91-76T>C | intron_variant | ENST00000299506.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUB | ENST00000299506.3 | c.91-76T>C | intron_variant | 1 | NM_177972.3 | P1 | |||
TUB | ENST00000305253.8 | c.256-76T>C | intron_variant | 1 | |||||
TUB | ENST00000534099.5 | c.109-76T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.638 AC: 97045AN: 152062Hom.: 31292 Cov.: 35
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GnomAD4 exome AF: 0.670 AC: 888682AN: 1325672Hom.: 299099 AF XY: 0.669 AC XY: 431898AN XY: 645854
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GnomAD4 genome AF: 0.638 AC: 97085AN: 152180Hom.: 31299 Cov.: 35 AF XY: 0.637 AC XY: 47394AN XY: 74406
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at