Genetic Variant OPRD1:p.Gly307Gly (chr1-28863085-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_000911.4(OPRD1):c.921C>T(p.Gly307Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 1,607,094 control chromosomes in the GnomAD database, including 255,002 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 0.51 ( 21057 hom., cov: 34)

Exomes 𝑓: 0.56 ( 233945 hom. )

Consequence

OPRD1
NM_000911.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.399

Publications

74 publications found

Variant links:

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]

OPRD1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP7

Synonymous conserved (PhyloP=0.399 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPRD1	NM_000911.4 link	c.921C>T	p.Gly307Gly	synonymous_variant	Exon 3 of 3	ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7 link	c.921C>T	p.Gly307Gly	synonymous_variant	Exon 3 of 3	1	NM_000911.4	ENSP00000234961.2

Frequencies

GnomAD3 genomes

AF:

0.511

AC:

77752

AN:

152056

Hom.:

21044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.430

Gnomad AMR

AF:

0.637

Gnomad ASJ

AF:

0.474

Gnomad EAS

AF:

0.773

Gnomad SAS

AF:

0.698

Gnomad FIN

AF:

0.582

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.547

Gnomad OTH

AF:

0.506

GnomAD2 exomes

AF:

0.589

AC:

141859

AN:

240868

AF XY:

0.589

show subpopulations

Gnomad AFR exome

AF:

0.334

Gnomad AMR exome

AF:

0.717

Gnomad ASJ exome

AF:

0.467

Gnomad EAS exome

AF:

0.768

Gnomad FIN exome

AF:

0.572

Gnomad NFE exome

AF:

0.543

Gnomad OTH exome

AF:

0.565

GnomAD4 exome

AF:

0.562

AC:

817470

AN:

1454920

Hom.:

233945

Cov.:

AF XY:

0.565

AC XY:

408802

AN XY:

723418

show subpopulations

African (AFR)

AF:

0.329

AC:

10991

AN:

33368

American (AMR)

AF:

0.710

AC:

31234

AN:

43978

Ashkenazi Jewish (ASJ)

AF:

0.468

AC:

12133

AN:

25914

East Asian (EAS)

AF:

0.786

AC:

31018

AN:

39464

South Asian (SAS)

AF:

0.690

AC:

59083

AN:

85666

European-Finnish (FIN)

AF:

0.570

AC:

29351

AN:

51476

Middle Eastern (MID)

AF:

0.486

AC:

2792

AN:

5750

European-Non Finnish (NFE)

AF:

0.548

AC:

607468

AN:

1109198

Other (OTH)

AF:

0.556

AC:

33400

AN:

60106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

21866

43732

65599

87465

109331

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17242

34484

51726

68968

86210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.511

AC:

77799

AN:

152174

Hom.:

21057

Cov.:

AF XY:

0.523

AC XY:

38888

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.340

AC:

14118

AN:

41536

American (AMR)

AF:

0.637

AC:

9751

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.474

AC:

1645

AN:

3470

East Asian (EAS)

AF:

0.772

AC:

3993

AN:

5170

South Asian (SAS)

AF:

0.697

AC:

3364

AN:

4828

European-Finnish (FIN)

AF:

0.582

AC:

6167

AN:

10604

Middle Eastern (MID)

AF:

0.441

AC:

128

AN:

290

European-Non Finnish (NFE)

AF:

0.547

AC:

37164

AN:

67956

Other (OTH)

AF:

0.510

AC:

1079

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1862

3723

5585

7446

9308

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

694

1388

2082

2776

3470

<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:

0.538

Hom.:

10742

Bravo

AF:

0.505

Asia WGS

AF:

0.687

AC:

2390

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

(source)

DANN

Benign

0.90

PhyloP100

0.40

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over