chr1-28813244-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000911.4(OPRD1):c.227+634G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,164 control chromosomes in the GnomAD database, including 3,189 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.
Frequency
Genomes: 𝑓 0.19 ( 3189 hom., cov: 32)
Consequence
OPRD1
NM_000911.4 intron
NM_000911.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.94
Publications
32 publications found
Genes affected
OPRD1 (HGNC:8153): (opioid receptor delta 1) Enables G protein-coupled enkephalin receptor activity. Involved in several processes, including G protein-coupled opioid receptor signaling pathway; cellular response to hypoxia; and positive regulation of peptidyl-serine phosphorylation. Is intrinsic component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.189 AC: 28763AN: 152046Hom.: 3190 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
28763
AN:
152046
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.189 AC: 28768AN: 152164Hom.: 3189 Cov.: 32 AF XY: 0.192 AC XY: 14290AN XY: 74386 show subpopulations
GnomAD4 genome
AF:
AC:
28768
AN:
152164
Hom.:
Cov.:
32
AF XY:
AC XY:
14290
AN XY:
74386
show subpopulations
African (AFR)
AF:
AC:
3440
AN:
41530
American (AMR)
AF:
AC:
2987
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
798
AN:
3470
East Asian (EAS)
AF:
AC:
543
AN:
5182
South Asian (SAS)
AF:
AC:
767
AN:
4826
European-Finnish (FIN)
AF:
AC:
3255
AN:
10566
Middle Eastern (MID)
AF:
AC:
67
AN:
294
European-Non Finnish (NFE)
AF:
AC:
16271
AN:
67984
Other (OTH)
AF:
AC:
442
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1181
2362
3544
4725
5906
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
306
612
918
1224
1530
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
457
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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