2-101022316-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001330348.2(TBC1D8):c.2726A>C(p.Gln909Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,612,648 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001330348.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D8 | NM_001330348.2 | c.2726A>C | p.Gln909Pro | missense_variant | 16/20 | ENST00000409318.2 | |
TBC1D8 | NM_001102426.3 | c.2681A>C | p.Gln894Pro | missense_variant | 16/20 | ||
TBC1D8 | NR_138475.2 | n.2692A>C | non_coding_transcript_exon_variant | 15/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D8 | ENST00000409318.2 | c.2726A>C | p.Gln909Pro | missense_variant | 16/20 | 5 | NM_001330348.2 | A1 | |
TBC1D8 | ENST00000376840.8 | c.2681A>C | p.Gln894Pro | missense_variant | 16/20 | 1 | P4 | ||
RPL31 | ENST00000441435.1 | c.310-1309T>G | intron_variant | 2 | |||||
TBC1D8 | ENST00000494011.1 | n.58A>C | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000236 AC: 36AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000377 AC: 93AN: 246660Hom.: 1 AF XY: 0.000403 AC XY: 54AN XY: 134008
GnomAD4 exome AF: 0.000206 AC: 301AN: 1460404Hom.: 2 Cov.: 30 AF XY: 0.000224 AC XY: 163AN XY: 726538
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.2681A>C (p.Q894P) alteration is located in exon 16 (coding exon 16) of the TBC1D8 gene. This alteration results from a A to C substitution at nucleotide position 2681, causing the glutamine (Q) at amino acid position 894 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at