chr6-154124080-A-G

Variant names:

• chr6-154124080-A-G
• rs10485058
• NM_000914.5:c.*5359A>G

Variant summary

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

The NM_000914.5(OPRM1):​c.*5359A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,192 control chromosomes in the GnomAD database, including 1,245 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 0.11 (1245 hom., cov: 32)
• Consequence: OPRM1 NM_000914.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 31 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000914.5. 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
	OPRM1	NM_000914.5	MANE Select	c.*5359A>G		3_prime_UTR	Exon 4 of 4	NP_000905.3	P35372-1
	OPRM1	NM_001145279.4		c.*5359A>G		3_prime_UTR	Exon 6 of 6	NP_001138751.1	P35372-10
	OPRM1	NM_001285524.1		c.*5359A>G		3_prime_UTR	Exon 5 of 5	NP_001272453.1	P35372-10

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPRM1	ENST00000330432.12	TSL:1 MANE Select	c.*5359A>G		3_prime_UTR	Exon 4 of 4	ENSP00000328264.7	P35372-1
	OPRM1	ENST00000337049.8	TSL:1	c.1164+32608A>G		intron	N/A	ENSP00000338381.4	P35372-5
	OPRM1	ENST00000524150.2	TSL:5	n.*250+32608A>G		intron	N/A	ENSP00000430575.1	P35372-18

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17502 AN: 152074 Hom.: 1246 Cov.: 32

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.0750

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.115 AC: 17502 AN: 152192 Hom.: 1245 Cov.: 32 AF XY: 0.118 AC XY: 8765 AN XY: 74402

African (AFR) AF: 0.0605 AC: 2511 AN: 41538

American (AMR) AF: 0.0910 AC: 1391 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0750 AC: 260 AN: 3468

East Asian (EAS) AF: 0.0380 AC: 197 AN: 5188

South Asian (SAS) AF: 0.0585 AC: 282 AN: 4822

European-Finnish (FIN) AF: 0.260 AC: 2747 AN: 10576

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9787 AN: 67992

Other (OTH) AF: 0.113 AC: 238 AN: 2112

Alfa AF: 0.126 Hom.: 4251

Bravo AF: 0.104

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.69
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10485058; hg19: chr6-154445215;