17-31295541-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002544.5(OMG):āc.791A>Gā(p.His264Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002544.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OMG | NM_002544.5 | c.791A>G | p.His264Arg | missense_variant | 2/2 | ENST00000247271.5 | NP_002535.3 | |
NF1 | NM_001042492.3 | c.4835+30202T>C | intron_variant | ENST00000358273.9 | NP_001035957.1 | |||
NF1 | NM_000267.3 | c.4772+30202T>C | intron_variant | NP_000258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OMG | ENST00000247271.5 | c.791A>G | p.His264Arg | missense_variant | 2/2 | 1 | NM_002544.5 | ENSP00000247271.4 | ||
NF1 | ENST00000358273.9 | c.4835+30202T>C | intron_variant | 1 | NM_001042492.3 | ENSP00000351015.4 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251342Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135834
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461816Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727210
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2024 | The c.791A>G (p.H264R) alteration is located in exon 2 (coding exon 1) of the OMG gene. This alteration results from a A to G substitution at nucleotide position 791, causing the histidine (H) at amino acid position 264 to be replaced by an arginine (R). 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