16-88706552-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001012759.3(CTU2):c.22T>A(p.Tyr8Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,459,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001012759.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.22T>A | p.Tyr8Asn | missense_variant | Exon 1 of 15 | ENST00000453996.7 | NP_001012777.1 | |
CTU2 | NM_001318507.2 | c.22T>A | p.Tyr8Asn | missense_variant | Exon 1 of 15 | NP_001305436.1 | ||
CTU2 | NM_001012762.3 | c.22T>A | p.Tyr8Asn | missense_variant | Exon 1 of 14 | NP_001012780.1 | ||
CTU2 | NM_001318513.2 | c.-161T>A | 5_prime_UTR_variant | Exon 1 of 14 | NP_001305442.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151940Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000153 AC: 2AN: 1307290Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 644908
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151940Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74206
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant has not been reported in the literature in individuals affected with CTU2-related conditions. 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). This variant is present in population databases (no rsID available, gnomAD 0.1%). This sequence change replaces tyrosine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 8 of the CTU2 protein (p.Tyr8Asn). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at