16-88706528-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001012759.3(CTU2):c.-3C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,449,456 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 Likely benign (no stars).
Frequency
Consequence
NM_001012759.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.-3C>G | 5_prime_UTR_variant | Exon 1 of 15 | ENST00000453996.7 | NP_001012777.1 | ||
CTU2 | NM_001318507.2 | c.-3C>G | 5_prime_UTR_variant | Exon 1 of 15 | NP_001305436.1 | |||
CTU2 | NM_001012762.3 | c.-3C>G | 5_prime_UTR_variant | Exon 1 of 14 | NP_001012780.1 | |||
CTU2 | NM_001318513.2 | c.-185C>G | 5_prime_UTR_variant | Exon 1 of 14 | NP_001305442.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000526 AC: 80AN: 152126Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000154 AC: 1AN: 65110Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 38576
GnomAD4 exome AF: 0.0000555 AC: 72AN: 1297222Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 37AN XY: 639754
GnomAD4 genome AF: 0.000526 AC: 80AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.000484 AC XY: 36AN XY: 74438
ClinVar
Submissions by phenotype
CTU2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at