chr10-27509877-T-A
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_021252.5(RAB18):c.71T>A(p.Leu24Gln) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000137 in 1,459,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. L24L) has been classified as Likely benign.
Frequency
Consequence
NM_021252.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB18 | NM_021252.5 | c.71T>A | p.Leu24Gln | missense_variant, splice_region_variant | 2/7 | ENST00000356940.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB18 | ENST00000356940.11 | c.71T>A | p.Leu24Gln | missense_variant, splice_region_variant | 2/7 | 1 | NM_021252.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251060Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135728
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459768Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726274
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Warburg micro syndrome 3 Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 08, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at