chr17-31296054-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_002544.5(OMG):c.278T>C(p.Leu93Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,066 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_002544.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OMG | NM_002544.5 | c.278T>C | p.Leu93Pro | missense_variant | 2/2 | ENST00000247271.5 | |
NF1 | NM_001042492.3 | c.4836-29766A>G | intron_variant | ENST00000358273.9 | |||
NF1 | NM_000267.3 | c.4773-29766A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OMG | ENST00000247271.5 | c.278T>C | p.Leu93Pro | missense_variant | 2/2 | 1 | NM_002544.5 | P1 | |
NF1 | ENST00000358273.9 | c.4836-29766A>G | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461752Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727172
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.278T>C (p.L93P) alteration is located in exon 2 (coding exon 1) of the OMG gene. This alteration results from a T to C substitution at nucleotide position 278, causing the leucine (L) at amino acid position 93 to be replaced by a proline (P). 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
Publications
No publications associated with this variant yet.