chr11-132959967-A-G

Variant names:

• chr11-132959967-A-G
• rs1567127
• NM_001012393.5:c.62-16957T>C

Variant summary

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

The NM_001012393.5(OPCML):​c.62-16957T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,074 control chromosomes in the GnomAD database, including 8,629 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 0.29 (8629 hom., cov: 32)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736
• Publications: 9 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]

LOC105369580 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPCML	NM_001012393.5	c.62-16957T>C		intron_variant	Intron 1 of 7	ENST00000524381.6	NP_001012393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPCML	ENST00000524381.6	c.62-16957T>C		intron_variant	Intron 1 of 7	1	NM_001012393.5	ENSP00000434750.1
OPCML	ENST00000529038.5	n.140-302648T>C		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44323 AN: 151956 Hom.: 8617 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0960

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.292 AC: 44363 AN: 152074 Hom.: 8629 Cov.: 32 AF XY: 0.287 AC XY: 21369 AN XY: 74340

African (AFR) AF: 0.560 AC: 23228 AN: 41454

American (AMR) AF: 0.183 AC: 2796 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3472

East Asian (EAS) AF: 0.0960 AC: 496 AN: 5166

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4818

European-Finnish (FIN) AF: 0.168 AC: 1777 AN: 10594

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13023 AN: 67972

Other (OTH) AF: 0.281 AC: 593 AN: 2112

Alfa AF: 0.218 Hom.: 18319

Bravo AF: 0.305

Asia WGS AF: 0.186 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.6
DANN	Benign	0.74
PhyloP100		0.74
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: rs1567127; hg19: chr11-132829862;