1-28858581-T-C

Variant names:

• chr1-28858581-T-C
• rs12404612
• NM_000911.4:c.228-373T>C

Variant summary

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

The NM_000911.4(OPRD1):​c.228-373T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 149,802 control chromosomes in the GnomAD database, including 1,083 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 0.095 (1083 hom., cov: 28)
• Consequence: OPRD1 NM_000911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPRD1	NM_000911.4	MANE Select	c.228-373T>C		intron	N/A	NP_000902.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPRD1	ENST00000234961.7	TSL:1 MANE Select	c.228-373T>C		intron	N/A	ENSP00000234961.2	P41143

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14172 AN: 149684 Hom.: 1088 Cov.: 28

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.0397

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0680

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0822

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0945 AC: 14160 AN: 149802 Hom.: 1083 Cov.: 28 AF XY: 0.0990 AC XY: 7228 AN XY: 73026

African (AFR) AF: 0.0489 AC: 1989 AN: 40678

American (AMR) AF: 0.137 AC: 2047 AN: 14982

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3456

East Asian (EAS) AF: 0.437 AC: 2160 AN: 4940

South Asian (SAS) AF: 0.238 AC: 1094 AN: 4600

European-Finnish (FIN) AF: 0.0680 AC: 705 AN: 10372

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0822 AC: 5550 AN: 67516

Other (OTH) AF: 0.0841 AC: 173 AN: 2058

Alfa AF: 0.0322 Hom.: 21

Bravo AF: 0.0993

Asia WGS AF: 0.283 AC: 983 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.40
PhyloP100		-0.072
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: rs12404612; hg19: chr1-29185093;