chr1-28820826-C-T

Variant names:

• chr1-28820826-C-T
• rs536706
• NM_000911.4:c.227+8216C>T

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+8216C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,556 control chromosomes in the GnomAD database, including 17,724 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 (17724 hom., cov: 29)
• Consequence: OPRD1 NM_000911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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.227+8216C>T		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.227+8216C>T		intron	N/A	ENSP00000234961.2	P41143
	ENSG00000305996	ENST00000814652.1		n.92-7097C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69241 AN: 151438 Hom.: 17717 Cov.: 29

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.457 AC: 69277 AN: 151556 Hom.: 17724 Cov.: 29 AF XY: 0.463 AC XY: 34269 AN XY: 74022

African (AFR) AF: 0.221 AC: 9145 AN: 41334

American (AMR) AF: 0.496 AC: 7553 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3466

East Asian (EAS) AF: 0.775 AC: 3931 AN: 5072

South Asian (SAS) AF: 0.655 AC: 3136 AN: 4786

European-Finnish (FIN) AF: 0.562 AC: 5915 AN: 10522

Middle Eastern (MID) AF: 0.400 AC: 116 AN: 290

European-Non Finnish (NFE) AF: 0.533 AC: 36157 AN: 67866

Other (OTH) AF: 0.438 AC: 916 AN: 2090

Alfa AF: 0.477 Hom.: 2430

Bravo AF: 0.435

Asia WGS AF: 0.669 AC: 2325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.20
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: rs536706; hg19: chr1-29147338;