9-135119924-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001282611.2(OLFM1):c.1204G>A(p.Ala402Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,400 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_001282611.2 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 |
---|---|---|---|---|---|---|---|---|
OLFM1 | NM_001282611.2 | c.1204G>A | p.Ala402Thr | missense_variant | Exon 6 of 6 | ENST00000371793.8 | NP_001269540.1 | |
OLFM1 | NM_014279.5 | c.1150G>A | p.Ala384Thr | missense_variant | Exon 6 of 6 | NP_055094.1 | ||
OLFM1 | NM_001282612.1 | c.1123G>A | p.Ala375Thr | missense_variant | Exon 6 of 6 | NP_001269541.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461198Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726904
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1150G>A (p.A384T) alteration is located in exon 6 (coding exon 6) of the OLFM1 gene. This alteration results from a G to A substitution at nucleotide position 1150, causing the alanine (A) at amino acid position 384 to be replaced by a threonine (T). 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