chr17-79942065-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019020.4(TBC1D16):c.2050C>T(p.Arg684Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,610,602 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R684Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_019020.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D16 | NM_019020.4 | c.2050C>T | p.Arg684Trp | missense_variant | 11/12 | ENST00000310924.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D16 | ENST00000310924.7 | c.2050C>T | p.Arg684Trp | missense_variant | 11/12 | 1 | NM_019020.4 | P1 | |
TBC1D16 | ENST00000340848.11 | c.964C>T | p.Arg322Trp | missense_variant | 7/8 | 1 | |||
TBC1D16 | ENST00000576768.5 | c.925C>T | p.Arg309Trp | missense_variant | 7/8 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000857 AC: 21AN: 244982Hom.: 0 AF XY: 0.0000600 AC XY: 8AN XY: 133306
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1458452Hom.: 0 Cov.: 33 AF XY: 0.0000262 AC XY: 19AN XY: 725322
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.2050C>T (p.R684W) alteration is located in exon 11 (coding exon 10) of the TBC1D16 gene. This alteration results from a C to T substitution at nucleotide position 2050, causing the arginine (R) at amino acid position 684 to be replaced by a tryptophan (W). 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