rs583664

Positions:

• chr6-154120092-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000914.5(OPRM1):​c.*1371T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,158 control chromosomes in the GnomAD database, including 3,201 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 0.20 (3201 hom., cov: 33)
• Consequence: OPRM1 NM_000914.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

OPRM1 (HGNC:8156): (opioid receptor mu 1) This gene encodes one of at least three opioid receptors in humans; the mu opioid receptor (MOR). The MOR is the principal target of endogenous opioid peptides and opioid analgesic agents such as beta-endorphin and enkephalins. The MOR also has an important role in dependence to other drugs of abuse, such as nicotine, cocaine, and alcohol via its modulation of the dopamine system. The NM_001008503.2:c.118A>G allele has been associated with opioid and alcohol addiction and variations in pain sensitivity but evidence for it having a causal role is conflicting. Multiple transcript variants encoding different isoforms have been found for this gene. Though the canonical MOR belongs to the superfamily of 7-transmembrane-spanning G-protein-coupled receptors some isoforms of this gene have only 6 transmembrane domains. [provided by RefSeq, Oct 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPRM1	NM_000914.5	c.*1371T>C		3_prime_UTR_variant	4/4	ENST00000330432.12	NP_000905.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPRM1	ENST00000330432.12	c.*1371T>C		3_prime_UTR_variant	4/4	1	NM_000914.5	ENSP00000328264	P1
OPRM1	ENST00000337049.8	c.1164+28620T>C		intron_variant		1		ENSP00000338381
OPRM1	ENST00000524150.2	c.*250+28620T>C		intron_variant, NMD_transcript_variant		5		ENSP00000430575

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29686 AN: 152040 Hom.: 3199 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0846

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.195 AC: 29715 AN: 152158 Hom.: 3201 Cov.: 33 AF XY: 0.190 AC XY: 14171 AN XY: 74402

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0847

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.182

Alfa AF: 0.225 Hom.: 512

Bravo AF: 0.191

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	9.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs583664; hg19: chr6-154441227;