chr16-88706555-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001012759.3(CTU2):c.25G>A(p.Gly9Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0181 in 1,458,604 control chromosomes in the GnomAD database, including 272 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001012759.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.25G>A | p.Gly9Arg | missense_variant | 1/15 | ENST00000453996.7 | |
CTU2 | NM_001318507.2 | c.25G>A | p.Gly9Arg | missense_variant | 1/15 | ||
CTU2 | NM_001012762.3 | c.25G>A | p.Gly9Arg | missense_variant | 1/14 | ||
CTU2 | NM_001318513.2 | c.-158G>A | 5_prime_UTR_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTU2 | ENST00000453996.7 | c.25G>A | p.Gly9Arg | missense_variant | 1/15 | 1 | NM_001012759.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0135 AC: 2055AN: 152032Hom.: 22 Cov.: 33
GnomAD3 exomes AF: 0.0152 AC: 1069AN: 70398Hom.: 13 AF XY: 0.0156 AC XY: 642AN XY: 41208
GnomAD4 exome AF: 0.0186 AC: 24330AN: 1306464Hom.: 250 Cov.: 31 AF XY: 0.0184 AC XY: 11835AN XY: 644460
GnomAD4 genome AF: 0.0135 AC: 2054AN: 152140Hom.: 22 Cov.: 33 AF XY: 0.0128 AC XY: 949AN XY: 74398
ClinVar
Submissions by phenotype
CTU2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at