19-9854566-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_058164.4(OLFM2):c.985G>A(p.Glu329Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,788 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 Uncertain significance (★).
Frequency
Consequence
NM_058164.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OLFM2 | NM_058164.4 | c.985G>A | p.Glu329Lys | missense_variant | Exon 6 of 6 | ENST00000264833.9 | NP_477512.1 | |
OLFM2 | NM_001304347.2 | c.1057G>A | p.Glu353Lys | missense_variant | Exon 6 of 6 | NP_001291276.1 | ||
OLFM2 | NM_001304348.2 | c.751G>A | p.Glu251Lys | missense_variant | Exon 5 of 5 | NP_001291277.1 | ||
OLFM2 | XM_047439713.1 | c.781G>A | p.Glu261Lys | missense_variant | Exon 6 of 6 | XP_047295669.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461596Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 727108
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.985G>A (p.E329K) alteration is located in exon 6 (coding exon 6) of the OLFM2 gene. This alteration results from a G to A substitution at nucleotide position 985, causing the glutamic acid (E) at amino acid position 329 to be replaced by a lysine (K). 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