dbSNP rs12271299: OPCML:c.62-267043G>A (chr11-133210053-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001012393.5(OPCML):c.62-267043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,086 control chromosomes in the GnomAD database, including 4,652 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 0.22 ( 4652 hom., cov: 32)

Consequence

OPCML
NM_001012393.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.664

Publications

5 publications found

Variant links:

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]

OPCML links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
OPCML	NM_001012393.5 link	c.62-267043G>A	intron_variant	Intron 1 of 7	ENST00000524381.6	NP_001012393.1
OPCML	NM_001319104.4 link	c.-134+322211G>A	intron_variant	Intron 1 of 6		NP_001306033.1
OPCML	XM_006718846.4 link	c.62-267043G>A	intron_variant	Intron 1 of 7		XP_006718909.1
OPCML	XM_047427032.1 link	c.-42+86971G>A	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 link	c.62-267043G>A		intron_variant	Intron 1 of 7	1	NM_001012393.5	ENSP00000434750.1
OPCML	ENST00000529038.5 link	n.139+322211G>A		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33576

AN:

151968

Hom.:

4648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0827

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.361

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.431

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.258

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

GnomAD4 genome

AF:

0.221

AC:

33587

AN:

152086

Hom.:

4652

Cov.:

AF XY:

0.229

AC XY:

17022

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.0825

AC:

3428

AN:

41536

American (AMR)

AF:

0.362

AC:

5524

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.386

AC:

1340

AN:

3468

East Asian (EAS)

AF:

0.430

AC:

2210

AN:

5136

South Asian (SAS)

AF:

0.350

AC:

1684

AN:

4816

European-Finnish (FIN)

AF:

0.274

AC:

2893

AN:

10572

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15649

AN:

67968

Other (OTH)

AF:

0.256

AC:

540

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1231

2461

3692

4922

6153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.234

Hom.:

13666

Bravo

AF:

0.226

Asia WGS

AF:

0.391

AC:

1355

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

0.26

(source)

DANN

Benign

0.84

PhyloP100

-0.66

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over