chr10-133279825-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006659.4(TUBGCP2):c.2650G>C(p.Val884Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP2 | NM_006659.4 | c.2650G>C | p.Val884Leu | missense_variant | 18/18 | ENST00000252936.8 | |
TUBGCP2 | NM_001256617.2 | c.2734G>C | p.Val912Leu | missense_variant | 19/19 | ||
TUBGCP2 | NM_001256618.2 | c.2260G>C | p.Val754Leu | missense_variant | 17/17 | ||
TUBGCP2 | NR_046330.2 | n.3370G>C | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP2 | ENST00000252936.8 | c.2650G>C | p.Val884Leu | missense_variant | 18/18 | 2 | NM_006659.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | The c.2650G>C (p.V884L) alteration is located in exon 18 (coding exon 17) of the TUBGCP2 gene. This alteration results from a G to C substitution at nucleotide position 2650, causing the valine (V) at amino acid position 884 to be replaced by a leucine (L). 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