chr1-28824671-G-A

Variant names:

• chr1-28824671-G-A
• rs797397
• NM_000911.4:c.227+12061G>A

Variant summary

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

The NM_000911.4(OPRD1):​c.227+12061G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,700 control chromosomes in the GnomAD database, including 17,976 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 0.46 (17976 hom., cov: 30)
• Consequence: OPRD1 NM_000911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524
• Publications: 8 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]

ENSG00000305996 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPRD1	NM_000911.4	c.227+12061G>A		intron_variant	Intron 1 of 2	ENST00000234961.7	NP_000902.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPRD1	ENST00000234961.7	c.227+12061G>A		intron_variant	Intron 1 of 2	1	NM_000911.4	ENSP00000234961.2
ENSG00000305996	ENST00000814652.1	n.92-3252G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69726 AN: 151582 Hom.: 17970 Cov.: 30

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.460 AC: 69759 AN: 151700 Hom.: 17976 Cov.: 30 AF XY: 0.468 AC XY: 34651 AN XY: 74084

African (AFR) AF: 0.222 AC: 9177 AN: 41380

American (AMR) AF: 0.500 AC: 7607 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1885 AN: 3468

East Asian (EAS) AF: 0.799 AC: 4114 AN: 5148

South Asian (SAS) AF: 0.684 AC: 3277 AN: 4792

European-Finnish (FIN) AF: 0.571 AC: 5986 AN: 10478

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36178 AN: 67904

Other (OTH) AF: 0.440 AC: 924 AN: 2098

Alfa AF: 0.514 Hom.: 88603

Bravo AF: 0.437

Asia WGS AF: 0.686 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.56
PhyloP100		0.52
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: rs797397; hg19: chr1-29151183;