rs2298897

Variant names:

• chr1-28839325-C-G
• rs2298897
• NM_000911.4:c.228-19629C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000911.4(OPRD1):​c.228-19629C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,004 control chromosomes in the GnomAD database, including 6,575 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 0.29 (6575 hom., cov: 32)
• Consequence: OPRD1 NM_000911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000911.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPRD1	NM_000911.4	MANE Select	c.228-19629C>G		intron	N/A	NP_000902.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPRD1	ENST00000234961.7	TSL:1 MANE Select	c.228-19629C>G		intron	N/A	ENSP00000234961.2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43710 AN: 151886 Hom.: 6574 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.321

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.288 AC: 43744 AN: 152004 Hom.: 6575 Cov.: 32 AF XY: 0.288 AC XY: 21398 AN XY: 74300

African (AFR) AF: 0.319 AC: 13220 AN: 41438

American (AMR) AF: 0.323 AC: 4929 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1230 AN: 3472

East Asian (EAS) AF: 0.100 AC: 518 AN: 5172

South Asian (SAS) AF: 0.200 AC: 961 AN: 4806

European-Finnish (FIN) AF: 0.297 AC: 3134 AN: 10560

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18735 AN: 67966

Other (OTH) AF: 0.319 AC: 674 AN: 2112

Alfa AF: 0.289 Hom.: 782

Bravo AF: 0.296

Asia WGS AF: 0.175 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.57
DANN	Benign	0.83
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2298897; hg19: chr1-29165837;