rs193920761
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020190.5(OLFML3):c.402C>A(p.Asp134Glu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000264 in 1,516,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_020190.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OLFML3 | NM_020190.5 | c.402C>A | p.Asp134Glu | missense_variant, splice_region_variant | 3/3 | ENST00000320334.5 | NP_064575.1 | |
OLFML3 | NM_001286352.3 | c.342C>A | p.Asp114Glu | missense_variant, splice_region_variant | 4/4 | NP_001273281.1 | ||
OLFML3 | NM_001286353.3 | c.219C>A | p.Asp73Glu | missense_variant, splice_region_variant | 3/3 | NP_001273282.1 | ||
OLFML3 | XM_017001848.3 | c.342C>A | p.Asp114Glu | missense_variant, splice_region_variant | 3/3 | XP_016857337.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OLFML3 | ENST00000320334.5 | c.402C>A | p.Asp134Glu | missense_variant, splice_region_variant | 3/3 | 1 | NM_020190.5 | ENSP00000322273.4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000562 AC: 1AN: 177808Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 93408
GnomAD4 exome AF: 0.00000220 AC: 3AN: 1364002Hom.: 0 Cov.: 31 AF XY: 0.00000300 AC XY: 2AN XY: 667714
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at