15-43403776-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014444.5(TUBGCP4):c.1825G>T(p.Ala609Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A609T) has been classified as Uncertain significance.
Frequency
Consequence
NM_014444.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP4 | NM_014444.5 | c.1825G>T | p.Ala609Ser | missense_variant | 16/18 | ENST00000564079.6 | |
TP53BP1 | NM_001141980.3 | c.*3607C>A | 3_prime_UTR_variant | 28/28 | ENST00000382044.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP4 | ENST00000564079.6 | c.1825G>T | p.Ala609Ser | missense_variant | 16/18 | 1 | NM_014444.5 | A1 | |
TP53BP1 | ENST00000382044.9 | c.*3607C>A | 3_prime_UTR_variant | 28/28 | 1 | NM_001141980.3 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249096Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135168
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461416Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727022
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 01, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with TUBGCP4-related conditions. This variant is present in population databases (rs770105036, ExAC 0.003%). This sequence change replaces alanine with serine at codon 610 of the TUBGCP4 protein (p.Ala610Ser). The alanine residue is moderately conserved and there is a moderate physicochemical difference between alanine and serine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at