chr11-133522399-G-T

Variant names:

• chr11-133522399-G-T
• rs7117082
• NM_001012393.5:c.61+9865C>A

Variant summary

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

The NM_001012393.5(OPCML):​c.61+9865C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,142 control chromosomes in the GnomAD database, including 6,262 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 0.21 (6262 hom., cov: 33)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 10 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012393.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPCML	NM_001012393.5	MANE Select	c.61+9865C>A		intron	N/A	NP_001012393.1
	OPCML	NM_001319104.4		c.-134+9865C>A		intron	N/A	NP_001306033.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPCML	ENST00000524381.6	TSL:1 MANE Select	c.61+9865C>A		intron	N/A	ENSP00000434750.1
	OPCML	ENST00000529038.5	TSL:5	n.139+9865C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32185 AN: 152024 Hom.: 6219 Cov.: 33

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0380

Gnomad EAS AF: 0.0778

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.212 AC: 32283 AN: 152142 Hom.: 6262 Cov.: 33 AF XY: 0.213 AC XY: 15814 AN XY: 74382

African (AFR) AF: 0.519 AC: 21503 AN: 41458

American (AMR) AF: 0.0963 AC: 1472 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0380 AC: 132 AN: 3470

East Asian (EAS) AF: 0.0780 AC: 404 AN: 5178

South Asian (SAS) AF: 0.190 AC: 916 AN: 4826

European-Finnish (FIN) AF: 0.154 AC: 1628 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0858 AC: 5836 AN: 68004

Other (OTH) AF: 0.159 AC: 337 AN: 2116

Alfa AF: 0.123 Hom.: 6136

Bravo AF: 0.218

Asia WGS AF: 0.161 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.028
DANN	Benign	0.67
PhyloP100		-1.7
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: rs7117082; hg19: chr11-133392294;