16-88707176-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_001012759.3(CTU2):āc.109G>Cā(p.Val37Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000805 in 1,613,950 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 (ā ).
Frequency
Consequence
NM_001012759.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.109G>C | p.Val37Leu | missense_variant | Exon 2 of 15 | ENST00000453996.7 | NP_001012777.1 | |
CTU2 | NM_001318507.2 | c.109G>C | p.Val37Leu | missense_variant | Exon 2 of 15 | NP_001305436.1 | ||
CTU2 | NM_001012762.3 | c.109G>C | p.Val37Leu | missense_variant | Exon 2 of 14 | NP_001012780.1 | ||
CTU2 | NM_001318513.2 | c.-74G>C | 5_prime_UTR_variant | Exon 2 of 14 | NP_001305442.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 250966Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135838
GnomAD4 exome AF: 0.0000800 AC: 117AN: 1461608Hom.: 0 Cov.: 32 AF XY: 0.0000853 AC XY: 62AN XY: 727080
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.109G>C (p.V37L) alteration is located in exon 2 (coding exon 2) of the CTU2 gene. This alteration results from a G to C substitution at nucleotide position 109, causing the valine (V) at amino acid position 37 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at