17-79941050-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_019020.4(TBC1D16):c.2113G>A(p.Asp705Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,450,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBC1D16 | ENST00000310924.7 | c.2113G>A | p.Asp705Asn | missense_variant | Exon 12 of 12 | 1 | NM_019020.4 | ENSP00000309794.2 | ||
TBC1D16 | ENST00000340848.11 | c.1027G>A | p.Asp343Asn | missense_variant | Exon 8 of 8 | 1 | ENSP00000341517.7 | |||
TBC1D16 | ENST00000576768.5 | c.988G>A | p.Asp330Asn | missense_variant | Exon 8 of 8 | 1 | ENSP00000461522.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000880 AC: 2AN: 227252Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 123694
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1450090Hom.: 0 Cov.: 32 AF XY: 0.0000153 AC XY: 11AN XY: 720284
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2113G>A (p.D705N) 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 2113, causing the aspartic acid (D) at amino acid position 705 to be replaced by an asparagine (N). 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