rs11686264
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001330348.2(TBC1D8):c.127+17666T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 152,074 control chromosomes in the GnomAD database, including 129 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 0.034 ( 129 hom., cov: 31)
Consequence
TBC1D8
NM_001330348.2 intron
NM_001330348.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.241
Genes affected
TBC1D8 (HGNC:17791): (TBC1 domain family member 8) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to be located in 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=-0.93).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0345 (5245/152074) while in subpopulation NFE AF= 0.0491 (3336/67978). AF 95% confidence interval is 0.0477. There are 129 homozygotes in gnomad4. There are 2594 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 130 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D8 | NM_001330348.2 | c.127+17666T>C | intron_variant | ENST00000409318.2 | |||
TBC1D8 | NM_001102426.3 | c.127+17666T>C | intron_variant | ||||
TBC1D8 | NR_138475.2 | n.256+17666T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D8 | ENST00000409318.2 | c.127+17666T>C | intron_variant | 5 | NM_001330348.2 | A1 | |||
TBC1D8 | ENST00000376840.8 | c.127+17666T>C | intron_variant | 1 | P4 | ||||
TBC1D8 | ENST00000463469.5 | n.450-43097T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0345 AC: 5247AN: 151956Hom.: 130 Cov.: 31
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0345 AC: 5245AN: 152074Hom.: 129 Cov.: 31 AF XY: 0.0349 AC XY: 2594AN XY: 74348
GnomAD4 genome
?
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31
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74348
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61
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3478
ClinVar
Not reported inComputational scores
Source:
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