rs143000899
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_024589.3(ROGDI):c.567G>T(p.Leu189=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L189L) has been classified as Likely benign.
Frequency
Consequence
NM_024589.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROGDI | NM_024589.3 | c.567G>T | p.Leu189= | synonymous_variant | 8/11 | ENST00000322048.12 | |
ROGDI | XM_006720947.5 | c.567G>T | p.Leu189= | synonymous_variant | 8/11 | ||
ROGDI | XM_047434636.1 | c.297G>T | p.Leu99= | synonymous_variant | 6/9 | ||
ROGDI | NR_046480.2 | n.574G>T | non_coding_transcript_exon_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROGDI | ENST00000322048.12 | c.567G>T | p.Leu189= | synonymous_variant | 8/11 | 1 | NM_024589.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249622Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135344
GnomAD4 exome Cov.: 36
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at