3-186555051-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018138.5(TBCCD1):c.893G>A(p.Cys298Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,458,266 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018138.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBCCD1 | NM_018138.5 | c.893G>A | p.Cys298Tyr | missense_variant | Exon 5 of 8 | ENST00000338733.10 | NP_060608.1 | |
TBCCD1 | NM_001134415.1 | c.893G>A | p.Cys298Tyr | missense_variant | Exon 5 of 8 | NP_001127887.1 | ||
TBCCD1 | NM_001286749.2 | c.605G>A | p.Cys202Tyr | missense_variant | Exon 4 of 7 | NP_001273678.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBCCD1 | ENST00000338733.10 | c.893G>A | p.Cys298Tyr | missense_variant | Exon 5 of 8 | 1 | NM_018138.5 | ENSP00000341652.5 | ||
TBCCD1 | ENST00000424280.5 | c.893G>A | p.Cys298Tyr | missense_variant | Exon 5 of 8 | 5 | ENSP00000411253.1 | |||
TBCCD1 | ENST00000446782.5 | c.605G>A | p.Cys202Tyr | missense_variant | Exon 4 of 7 | 2 | ENSP00000397091.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247724Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133874
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1458266Hom.: 0 Cov.: 32 AF XY: 0.00000414 AC XY: 3AN XY: 725294
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.893G>A (p.C298Y) alteration is located in exon 5 (coding exon 4) of the TBCCD1 gene. This alteration results from a G to A substitution at nucleotide position 893, causing the cysteine (C) at amino acid position 298 to be replaced by a tyrosine (Y). 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