6-154118046-A-G

Variant names:

• chr6-154118046-A-G
• rs1323041
• NM_000914.5:c.1165-637A>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.1165-637A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,018 control chromosomes in the GnomAD database, including 20,448 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 0.51 (20448 hom., cov: 32)
• Consequence: OPRM1 NM_000914.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPRM1	NM_000914.5	c.1165-637A>G		intron_variant	Intron 3 of 3	ENST00000330432.12	NP_000905.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPRM1	ENST00000330432.12	c.1165-637A>G		intron_variant	Intron 3 of 3	1	NM_000914.5	ENSP00000328264.7

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77875 AN: 151900 Hom.: 20454 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.512 AC: 77884 AN: 152018 Hom.: 20448 Cov.: 32 AF XY: 0.519 AC XY: 38579 AN XY: 74296

African (AFR) AF: 0.431 AC: 17880 AN: 41490

American (AMR) AF: 0.496 AC: 7569 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1958 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4099 AN: 5158

South Asian (SAS) AF: 0.653 AC: 3141 AN: 4808

European-Finnish (FIN) AF: 0.592 AC: 6245 AN: 10552

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.519 AC: 35276 AN: 67956

Other (OTH) AF: 0.539 AC: 1138 AN: 2110

Alfa AF: 0.494 Hom.: 5699

Bravo AF: 0.503

Asia WGS AF: 0.700 AC: 2434 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		-0.31
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: rs1323041; hg19: chr6-154439181; COSMIC: COSV57831741;