15-23005536-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_052903.6(TUBGCP5):c.2608G>A(p.Gly870Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,132 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_052903.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBGCP5 | ENST00000615383.5 | c.2608G>A | p.Gly870Arg | missense_variant | Exon 19 of 23 | 1 | NM_052903.6 | ENSP00000480316.1 | ||
TUBGCP5 | ENST00000620435.4 | c.2608G>A | p.Gly870Arg | missense_variant | Exon 19 of 22 | 2 | ENSP00000481853.1 | |||
TUBGCP5 | ENST00000610294.1 | c.571G>A | p.Gly191Arg | missense_variant | Exon 5 of 5 | 5 | ENSP00000483015.1 | |||
TUBGCP5 | ENST00000614508.4 | n.2608G>A | non_coding_transcript_exon_variant | Exon 19 of 24 | 5 | ENSP00000484566.1 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251426Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135896
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727246
GnomAD4 genome AF: 0.000289 AC: 44AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2608G>A (p.G870R) alteration is located in exon 19 (coding exon 19) of the TUBGCP5 gene. This alteration results from a G to A substitution at nucleotide position 2608, causing the glycine (G) at amino acid position 870 to be replaced by an arginine (R). 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