chr10-133281283-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006659.4(TUBGCP2):c.2563G>A(p.Val855Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,611,084 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBGCP2 | NM_006659.4 | c.2563G>A | p.Val855Ile | missense_variant | Exon 17 of 18 | ENST00000252936.8 | NP_006650.1 | |
TUBGCP2 | NM_001256617.2 | c.2647G>A | p.Val883Ile | missense_variant | Exon 18 of 19 | NP_001243546.1 | ||
TUBGCP2 | NM_001256618.2 | c.2173G>A | p.Val725Ile | missense_variant | Exon 16 of 17 | NP_001243547.1 | ||
TUBGCP2 | NR_046330.2 | n.3283G>A | non_coding_transcript_exon_variant | Exon 17 of 18 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000682 AC: 17AN: 249272Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 135008
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1458806Hom.: 0 Cov.: 31 AF XY: 0.00000827 AC XY: 6AN XY: 725716
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2563G>A (p.V855I) alteration is located in exon 17 (coding exon 16) of the TUBGCP2 gene. This alteration results from a G to A substitution at nucleotide position 2563, causing the valine (V) at amino acid position 855 to be replaced by an isoleucine (I). 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