16-88707120-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001012759.3(CTU2):c.69-16C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,611,542 control chromosomes in the GnomAD database, including 56,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001012759.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.69-16C>A | intron_variant | Intron 1 of 14 | ENST00000453996.7 | NP_001012777.1 | ||
CTU2 | NM_001318507.2 | c.69-16C>A | intron_variant | Intron 1 of 14 | NP_001305436.1 | |||
CTU2 | NM_001012762.3 | c.69-16C>A | intron_variant | Intron 1 of 13 | NP_001012780.1 | |||
CTU2 | NM_001318513.2 | c.-114-16C>A | intron_variant | Intron 1 of 13 | NP_001305442.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.194 AC: 29420AN: 151992Hom.: 3651 Cov.: 32
GnomAD3 exomes AF: 0.218 AC: 54667AN: 250640Hom.: 7242 AF XY: 0.230 AC XY: 31174AN XY: 135696
GnomAD4 exome AF: 0.260 AC: 378972AN: 1459432Hom.: 52537 Cov.: 32 AF XY: 0.262 AC XY: 190195AN XY: 725804
GnomAD4 genome AF: 0.193 AC: 29417AN: 152110Hom.: 3650 Cov.: 32 AF XY: 0.190 AC XY: 14149AN XY: 74350
ClinVar
Submissions by phenotype
not provided Benign:3
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CTU2-related disorder Benign:1
This variant is classified as 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