chr18-57435775-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004852.3(ONECUT2):āc.59T>Cā(p.Met20Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000268 in 1,119,318 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 ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M20V) has been classified as Uncertain significance.
Frequency
Consequence
NM_004852.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ONECUT2 | NM_004852.3 | c.59T>C | p.Met20Thr | missense_variant | 1/2 | ENST00000491143.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ONECUT2 | ENST00000491143.3 | c.59T>C | p.Met20Thr | missense_variant | 1/2 | 1 | NM_004852.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 0.00000268 AC: 3AN: 1119318Hom.: 0 Cov.: 32 AF XY: 0.00000541 AC XY: 3AN XY: 554654
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 30, 2022 | The c.59T>C (p.M20T) alteration is located in exon 1 (coding exon 1) of the ONECUT2 gene. This alteration results from a T to C substitution at nucleotide position 59, causing the methionine (M) at amino acid position 20 to be replaced by a threonine (T). 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