rs77476023
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000912.5(OPRK1):āc.598A>Gā(p.Lys200Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,609,364 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_000912.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPRK1 | NM_000912.5 | c.598A>G | p.Lys200Glu | missense_variant | 3/4 | ENST00000265572.8 | |
OPRK1 | NM_001318497.2 | c.598A>G | p.Lys200Glu | missense_variant | 3/4 | ||
OPRK1 | NM_001282904.2 | c.331A>G | p.Lys111Glu | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRK1 | ENST00000265572.8 | c.598A>G | p.Lys200Glu | missense_variant | 3/4 | 1 | NM_000912.5 | P1 | |
ENST00000524425.1 | n.671-7757T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00161 AC: 245AN: 152204Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000423 AC: 106AN: 250784Hom.: 0 AF XY: 0.000354 AC XY: 48AN XY: 135492
GnomAD4 exome AF: 0.000152 AC: 222AN: 1457042Hom.: 0 Cov.: 31 AF XY: 0.000140 AC XY: 101AN XY: 723682
GnomAD4 genome ? AF: 0.00161 AC: 245AN: 152322Hom.: 1 Cov.: 33 AF XY: 0.00149 AC XY: 111AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at