rs13936
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015043.4(TBC1D9B):c.*789C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 446,016 control chromosomes in the GnomAD database, including 6,627 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 0.098 ( 1269 hom., cov: 33)
Exomes 𝑓: 0.15 ( 5358 hom. )
Consequence
TBC1D9B
NM_015043.4 3_prime_UTR
NM_015043.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.159
Genes affected
TBC1D9B (HGNC:29097): (TBC1 domain family member 9B) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D9B | NM_015043.4 | c.*789C>T | 3_prime_UTR_variant | 21/21 | ENST00000355235.8 | ||
TBC1D9B | NM_198868.3 | c.*789C>T | 3_prime_UTR_variant | 22/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D9B | ENST00000355235.8 | c.*789C>T | 3_prime_UTR_variant | 21/21 | 5 | NM_015043.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0979 AC: 14901AN: 152138Hom.: 1264 Cov.: 33
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GnomAD4 exome AF: 0.152 AC: 44610AN: 293760Hom.: 5358 Cov.: 0 AF XY: 0.159 AC XY: 26370AN XY: 165496
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GnomAD4 genome ? AF: 0.0980 AC: 14914AN: 152256Hom.: 1269 Cov.: 33 AF XY: 0.108 AC XY: 8073AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at