15-52789236-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004498.4(ONECUT1):c.649G>A(p.Gly217Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000129 in 1,553,374 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 (★).
Frequency
Consequence
NM_004498.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ONECUT1 | ENST00000305901.7 | c.649G>A | p.Gly217Ser | missense_variant | Exon 1 of 2 | 1 | NM_004498.4 | ENSP00000302630.4 | ||
ONECUT1 | ENST00000570208.2 | n.160G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | ENSP00000476168.1 | ||||
ONECUT1 | ENST00000561401.3 | n.50+1793G>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151940Hom.: 0 Cov.: 32
GnomAD4 exome AF: 7.14e-7 AC: 1AN: 1401434Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 690612
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151940Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74184
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.649G>A (p.G217S) alteration is located in exon 1 (coding exon 1) of the ONECUT1 gene. This alteration results from a G to A substitution at nucleotide position 649, causing the glycine (G) at amino acid position 217 to be replaced by a serine (S). 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