16-88706598-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001012759.3(CTU2):āc.68G>Cā(p.Ser23Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000523 in 1,432,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001012759.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.68G>C | p.Ser23Thr | missense_variant, splice_region_variant | 1/15 | ENST00000453996.7 | |
CTU2 | NM_001318507.2 | c.68G>C | p.Ser23Thr | missense_variant, splice_region_variant | 1/15 | ||
CTU2 | NM_001012762.3 | c.68G>C | p.Ser23Thr | missense_variant, splice_region_variant | 1/14 | ||
CTU2 | NM_001318513.2 | c.-115G>C | splice_region_variant, 5_prime_UTR_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTU2 | ENST00000453996.7 | c.68G>C | p.Ser23Thr | missense_variant, splice_region_variant | 1/15 | 1 | NM_001012759.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152048Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000125 AC: 6AN: 47850Hom.: 0 AF XY: 0.000103 AC XY: 3AN XY: 29042
GnomAD4 exome AF: 0.0000453 AC: 58AN: 1280534Hom.: 0 Cov.: 31 AF XY: 0.0000492 AC XY: 31AN XY: 630358
GnomAD4 genome AF: 0.000112 AC: 17AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74402
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 15, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at