1-161983908-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_015441.3(OLFML2B):c.2020G>A(p.Gly674Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,614,086 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G674D) has been classified as Likely pathogenic.
Frequency
Consequence
NM_015441.3 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 |
---|---|---|---|---|---|---|---|---|
OLFML2B | NM_015441.3 | c.2020G>A | p.Gly674Ser | missense_variant | Exon 8 of 8 | ENST00000294794.8 | NP_056256.1 | |
OLFML2B | NM_001347700.2 | c.2026G>A | p.Gly676Ser | missense_variant | Exon 8 of 8 | NP_001334629.1 | ||
OLFML2B | NM_001297713.2 | c.2023G>A | p.Gly675Ser | missense_variant | Exon 8 of 8 | NP_001284642.1 | ||
OLFML2B | XM_011509398.3 | c.1300G>A | p.Gly434Ser | missense_variant | Exon 5 of 5 | XP_011507700.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152194Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727246
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2020G>A (p.G674S) alteration is located in exon 8 (coding exon 8) of the OLFML2B gene. This alteration results from a G to A substitution at nucleotide position 2020, causing the glycine (G) at amino acid position 674 to be replaced by a serine (S). 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