chr20-64097919-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_182647.4(OPRL1):c.351G>A(p.Pro117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,613,632 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.016 ( 64 hom., cov: 33)
Exomes 𝑓: 0.0022 ( 50 hom. )
Consequence
OPRL1
NM_182647.4 synonymous
NM_182647.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.10
Genes affected
OPRL1 (HGNC:8155): (opioid related nociceptin receptor 1) The protein encoded by this gene is a member of the 7 transmembrane-spanning G protein-coupled receptor family, and functions as a receptor for the endogenous, opioid-related neuropeptide, nociceptin/orphanin FQ. This receptor-ligand system modulates a variety of biological functions and neurobehavior, including stress responses and anxiety behavior, learning and memory, locomotor activity, and inflammatory and immune responses. A promoter region between this gene and the 5'-adjacent RGS19 (regulator of G-protein signaling 19) gene on the opposite strand functions bi-directionally as a core-promoter for both genes, suggesting co-operative transcriptional regulation of these two functionally related genes. Alternatively spliced transcript variants have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Dec 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 20-64097919-G-A is Benign according to our data. Variant chr20-64097919-G-A is described in ClinVar as [Benign]. Clinvar id is 777612.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.1 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0513 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPRL1 | NM_182647.4 | c.351G>A | p.Pro117= | synonymous_variant | 4/5 | ENST00000336866.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPRL1 | ENST00000336866.7 | c.351G>A | p.Pro117= | synonymous_variant | 4/5 | 5 | NM_182647.4 | P1 | |
ENST00000660961.1 | n.3064C>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.0160 AC: 2433AN: 152184Hom.: 62 Cov.: 33
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GnomAD3 exomes AF: 0.00460 AC: 1153AN: 250922Hom.: 26 AF XY: 0.00347 AC XY: 471AN XY: 135834
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GnomAD4 exome AF: 0.00223 AC: 3265AN: 1461330Hom.: 50 Cov.: 32 AF XY: 0.00199 AC XY: 1450AN XY: 726950
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GnomAD4 genome ? AF: 0.0160 AC: 2436AN: 152302Hom.: 64 Cov.: 33 AF XY: 0.0151 AC XY: 1124AN XY: 74480
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at