Genetic Variant IPCEF1:c.246+59A>C (chr6-154246532-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001130700.2(IPCEF1):c.246+59A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 1,521,538 control chromosomes in the GnomAD database, including 123,986 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).

Frequency

Genomes: 𝑓 0.36 ( 10488 hom., cov: 32)

Exomes 𝑓: 0.40 ( 113498 hom. )

Consequence

IPCEF1
NM_001130700.2 intron

Scores

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: -0.913

Variant links:

Genes affected

IPCEF1 (HGNC:21204): (interaction protein for cytohesin exchange factors 1) Predicted to enable peroxidase activity. Predicted to be involved in response to oxidative stress. Predicted to be located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

IPCEF1 links:

ENSG00000288520 (HGNC:):

ENSG00000288520 links:

OPRM1 (HGNC:8156): (opioid receptor mu 1) This gene encodes one of at least three opioid receptors in humans; the mu opioid receptor (MOR). The MOR is the principal target of endogenous opioid peptides and opioid analgesic agents such as beta-endorphin and enkephalins. The MOR also has an important role in dependence to other drugs of abuse, such as nicotine, cocaine, and alcohol via its modulation of the dopamine system. The NM_001008503.2:c.118A>G allele has been associated with opioid and alcohol addiction and variations in pain sensitivity but evidence for it having a causal role is conflicting. Multiple transcript variants encoding different isoforms have been found for this gene. Though the canonical MOR belongs to the superfamily of 7-transmembrane-spanning G-protein-coupled receptors some isoforms of this gene have only 6 transmembrane domains. [provided by RefSeq, Oct 2013]

OPRM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IPCEF1	NM_001130700.2 link	c.246+59A>C		intron_variant	Intron 5 of 11	ENST00000367220.9	NP_001124172.1	Q8WWN9-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IPCEF1	ENST00000367220.9 link	c.246+59A>C		intron_variant	Intron 5 of 11	2	NM_001130700.2	ENSP00000356189.4		Q8WWN9-2
ENSG00000288520	ENST00000673182.1 link	c.1629+59A>C		intron_variant	Intron 15 of 21			ENSP00000499846.1

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

55278

AN:

151944

Hom.:

10491

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.415

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.554

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.415

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.418

Gnomad OTH

AF:

0.380

GnomAD4 exome

AF:

0.400

AC:

548311

AN:

1369476

Hom.:

113498

AF XY:

0.397

AC XY:

268360

AN XY:

676040

show subpopulations

Gnomad4 AFR exome

AF:

0.298

Gnomad4 AMR exome

AF:

0.234

Gnomad4 ASJ exome

AF:

0.540

Gnomad4 EAS exome

AF:

0.256

Gnomad4 SAS exome

AF:

0.234

Gnomad4 FIN exome

AF:

0.421

Gnomad4 NFE exome

AF:

0.422

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.364

AC:

55284

AN:

152062

Hom.:

10488

Cov.:

AF XY:

0.360

AC XY:

26752

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.554

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.415

Gnomad4 NFE

AF:

0.418

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.375

Hom.:

1611

Bravo

AF:

0.359

Asia WGS

AF:

0.242

AC:

842

AN:

3478

ClinVar

Significance: drug response

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Tramadol response

Other:1

Apr 28, 2018

Bruce Budowle Laboratory, University of North Texas Health Science Center

Significance: drug response

Review Status: no assertion criteria provided

Collection Method: research

- T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.77

DANN

Benign

0.26

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over