rs7129456

Variant names:

• chr11-132652648-G-A
• rs7129456
• NM_001012393.5:c.379+4439C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-132652648-G-A
• chr11-132652648-G-C
• chr11-132652648-G-T

Variant summary

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

The NM_001012393.5(OPCML):​c.379+4439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,176 control chromosomes in the GnomAD database, including 1,710 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 (1710 hom., cov: 33)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPCML	NM_001012393.5	c.379+4439C>T		intron_variant	Intron 3 of 7	ENST00000524381.6	NP_001012393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPCML	ENST00000524381.6	c.379+4439C>T		intron_variant	Intron 3 of 7	1	NM_001012393.5	ENSP00000434750.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16171 AN: 152058 Hom.: 1707 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0756

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

GnomAD4 genome AF: 0.106 AC: 16206 AN: 152176 Hom.: 1710 Cov.: 33 AF XY: 0.103 AC XY: 7677 AN XY: 74398

African (AFR) AF: 0.279 AC: 11580 AN: 41482

American (AMR) AF: 0.0713 AC: 1090 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.0552 AC: 266 AN: 4816

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10614

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0390 AC: 2654 AN: 68016

Other (OTH) AF: 0.0748 AC: 158 AN: 2112

Alfa AF: 0.0445 Hom.: 165

Bravo AF: 0.118

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.68
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7129456; hg19: chr11-132522543;