17-31296020-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002544.5(OMG):c.312G>A(p.Met104Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OMG | NM_002544.5 | c.312G>A | p.Met104Ile | missense_variant | 2/2 | ENST00000247271.5 | |
NF1 | NM_001042492.3 | c.4836-29800C>T | intron_variant | ENST00000358273.9 | |||
NF1 | NM_000267.3 | c.4773-29800C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OMG | ENST00000247271.5 | c.312G>A | p.Met104Ile | missense_variant | 2/2 | 1 | NM_002544.5 | P1 | |
NF1 | ENST00000358273.9 | c.4836-29800C>T | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251012Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135626
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461830Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727216
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.312G>A (p.M104I) alteration is located in exon 2 (coding exon 1) of the OMG gene. This alteration results from a G to A substitution at nucleotide position 312, causing the methionine (M) at amino acid position 104 to be replaced by an isoleucine (I). 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