rs1630675

Variant names:

• chr11-133226430-G-C
• rs1630675
• NM_001012393.5:c.62-283420C>G

Variant summary

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

The NM_001012393.5(OPCML):​c.62-283420C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,146 control chromosomes in the GnomAD database, including 20,251 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 0.48 (20251 hom., cov: 33)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 publications found

Genes affected

OPCML (HGNC:8143): (opioid binding protein/cell adhesion molecule like) This gene encodes a member of the IgLON subfamily in the immunoglobulin protein superfamily of proteins. The encoded preprotein is proteolytically processed to generate the mature protein. This protein is localized in the plasma membrane and may have an accessory role in opioid receptor function. This gene has an ortholog in rat and bovine. The opioid binding-cell adhesion molecule encoded by the rat gene binds opioid alkaloids in the presence of acidic lipids, exhibits selectivity for mu ligands and acts as a GPI-anchored protein. Since the encoded protein is highly conserved in species during evolution, it may have a fundamental role in mammalian systems. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Jan 2016]

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 = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPCML	NM_001012393.5	c.62-283420C>G		intron_variant	Intron 1 of 7	ENST00000524381.6	NP_001012393.1
OPCML	NM_001319104.4	c.-134+305834C>G		intron_variant	Intron 1 of 6		NP_001306033.1
OPCML	XM_006718846.4	c.62-283420C>G		intron_variant	Intron 1 of 7		XP_006718909.1
OPCML	XM_047427032.1	c.-42+70594C>G		intron_variant	Intron 1 of 7		XP_047282988.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPCML	ENST00000524381.6	c.62-283420C>G		intron_variant	Intron 1 of 7	1	NM_001012393.5	ENSP00000434750.1
OPCML	ENST00000529038.5	n.139+305834C>G		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72561 AN: 152028 Hom.: 20247 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.477 AC: 72557 AN: 152146 Hom.: 20251 Cov.: 33 AF XY: 0.477 AC XY: 35457 AN XY: 74380

African (AFR) AF: 0.187 AC: 7753 AN: 41510

American (AMR) AF: 0.496 AC: 7581 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1454 AN: 5154

South Asian (SAS) AF: 0.491 AC: 2369 AN: 4824

European-Finnish (FIN) AF: 0.640 AC: 6765 AN: 10576

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42997 AN: 67992

Other (OTH) AF: 0.510 AC: 1079 AN: 2116

Alfa AF: 0.553 Hom.: 3178

Bravo AF: 0.452

Asia WGS AF: 0.386 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.016
DANN	Benign	0.44
PhyloP100		-1.4
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: rs1630675; hg19: chr11-133096325;