10-133282255-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006659.4(TUBGCP2):c.2377G>A(p.Glu793Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,611,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006659.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP2 | NM_006659.4 | c.2377G>A | p.Glu793Lys | missense_variant | 16/18 | ENST00000252936.8 | |
TUBGCP2 | NM_001256617.2 | c.2461G>A | p.Glu821Lys | missense_variant | 17/19 | ||
TUBGCP2 | NM_001256618.2 | c.1987G>A | p.Glu663Lys | missense_variant | 15/17 | ||
TUBGCP2 | NR_046330.2 | n.3097G>A | non_coding_transcript_exon_variant | 16/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP2 | ENST00000252936.8 | c.2377G>A | p.Glu793Lys | missense_variant | 16/18 | 2 | NM_006659.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000369 AC: 9AN: 243658Hom.: 0 AF XY: 0.0000376 AC XY: 5AN XY: 132942
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1459302Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 725928
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.2377G>A (p.E793K) alteration is located in exon 16 (coding exon 15) of the TUBGCP2 gene. This alteration results from a G to A substitution at nucleotide position 2377, causing the glutamic acid (E) at amino acid position 793 to be replaced by a lysine (K). 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