rs1799974
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP3BP4_ModerateBS2
The NM_000914.5(OPRM1):c.779G>A(p.Arg260His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000977 in 1,614,096 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R260C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000914.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPRM1 | NM_000914.5 | c.779G>A | p.Arg260His | missense_variant | 3/4 | ENST00000330432.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRM1 | ENST00000330432.12 | c.779G>A | p.Arg260His | missense_variant | 3/4 | 1 | NM_000914.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000973 AC: 148AN: 152104Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000677 AC: 169AN: 249576Hom.: 1 AF XY: 0.000709 AC XY: 96AN XY: 135406
GnomAD4 exome AF: 0.000978 AC: 1429AN: 1461874Hom.: 3 Cov.: 32 AF XY: 0.00103 AC XY: 746AN XY: 727242
GnomAD4 genome AF: 0.000972 AC: 148AN: 152222Hom.: 1 Cov.: 32 AF XY: 0.00103 AC XY: 77AN XY: 74428
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at