chr18-57435774-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004852.3(ONECUT2):c.58A>G(p.Met20Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000775 in 1,264,038 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M20T) has been classified as Uncertain significance.
Frequency
Consequence
NM_004852.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ONECUT2 | NM_004852.3 | c.58A>G | p.Met20Val | missense_variant | 1/2 | ENST00000491143.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ONECUT2 | ENST00000491143.3 | c.58A>G | p.Met20Val | missense_variant | 1/2 | 1 | NM_004852.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000829 AC: 12AN: 144752Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000148 AC: 27AN: 182318Hom.: 0 AF XY: 0.000155 AC XY: 16AN XY: 103036
GnomAD4 exome AF: 0.0000768 AC: 86AN: 1119286Hom.: 0 Cov.: 32 AF XY: 0.0000847 AC XY: 47AN XY: 554646
GnomAD4 genome ? AF: 0.0000829 AC: 12AN: 144752Hom.: 0 Cov.: 30 AF XY: 0.0000995 AC XY: 7AN XY: 70344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.58A>G (p.M20V) alteration is located in exon 1 (coding exon 1) of the ONECUT2 gene. This alteration results from a A to G substitution at nucleotide position 58, causing the methionine (M) at amino acid position 20 to be replaced by a valine (V). 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