chr10-133282246-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006659.4(TUBGCP2):c.2386G>A(p.Ala796Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000731 in 1,611,792 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006659.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP2 | NM_006659.4 | c.2386G>A | p.Ala796Thr | missense_variant | 16/18 | ENST00000252936.8 | |
TUBGCP2 | NM_001256617.2 | c.2470G>A | p.Ala824Thr | missense_variant | 17/19 | ||
TUBGCP2 | NM_001256618.2 | c.1996G>A | p.Ala666Thr | missense_variant | 15/17 | ||
TUBGCP2 | NR_046330.2 | n.3106G>A | non_coding_transcript_exon_variant | 16/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP2 | ENST00000252936.8 | c.2386G>A | p.Ala796Thr | missense_variant | 16/18 | 2 | NM_006659.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00319 AC: 486AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000912 AC: 223AN: 244500Hom.: 0 AF XY: 0.000720 AC XY: 96AN XY: 133260
GnomAD4 exome AF: 0.000474 AC: 692AN: 1459466Hom.: 3 Cov.: 31 AF XY: 0.000442 AC XY: 321AN XY: 726052
GnomAD4 genome ? AF: 0.00320 AC: 487AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.00293 AC XY: 218AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | TUBGCP2: BP4, BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at