chr15-52789079-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004498.4(ONECUT1):c.806G>A(p.Arg269Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,601,910 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R269G) has been classified as Uncertain significance.
Frequency
Consequence
NM_004498.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ONECUT1 | ENST00000305901.7 | c.806G>A | p.Arg269Gln | missense_variant | Exon 1 of 2 | 1 | NM_004498.4 | ENSP00000302630.4 | ||
ONECUT1 | ENST00000570208.2 | n.317G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | ENSP00000476168.1 | ||||
ONECUT1 | ENST00000561401.3 | n.50+1950G>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000248 AC: 6AN: 242320Hom.: 0 AF XY: 0.0000379 AC XY: 5AN XY: 131760
GnomAD4 exome AF: 0.0000235 AC: 34AN: 1449698Hom.: 0 Cov.: 31 AF XY: 0.0000319 AC XY: 23AN XY: 721694
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.806G>A (p.R269Q) 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 806, causing the arginine (R) at amino acid position 269 to be replaced by a glutamine (Q). 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