17-79940972-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019020.4(TBC1D16):c.2191G>A(p.Gly731Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000103 in 1,605,888 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019020.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBC1D16 | ENST00000310924.7 | c.2191G>A | p.Gly731Ser | missense_variant | Exon 12 of 12 | 1 | NM_019020.4 | ENSP00000309794.2 | ||
TBC1D16 | ENST00000340848.11 | c.1105G>A | p.Gly369Ser | missense_variant | Exon 8 of 8 | 1 | ENSP00000341517.7 | |||
TBC1D16 | ENST00000576768.5 | c.1066G>A | p.Gly356Ser | missense_variant | Exon 8 of 8 | 1 | ENSP00000461522.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000227 AC: 53AN: 233188Hom.: 1 AF XY: 0.000275 AC XY: 35AN XY: 127328
GnomAD4 exome AF: 0.000106 AC: 154AN: 1453660Hom.: 1 Cov.: 32 AF XY: 0.000145 AC XY: 105AN XY: 722524
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2191G>A (p.G731S) alteration is located in exon 12 (coding exon 11) of the TBC1D16 gene. This alteration results from a G to A substitution at nucleotide position 2191, causing the glycine (G) at amino acid position 731 to be replaced by a serine (S). 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