Variant rs2272381 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001130700.2(IPCEF1):c.321-29T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,583,206 control chromosomes in the GnomAD database, including 20,198 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.17 ( 2251 hom., cov: 33)

Exomes 𝑓: 0.16 ( 17947 hom. )

Consequence

IPCEF1
NM_001130700.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.67

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

This place is a probable branch point but rather VUS (scored 4 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IPCEF1	NM_001130700.2 linkuse as main transcript	c.321-29T>C		intron_variant		ENST00000367220.9	NP_001124172.1	Q8WWN9-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IPCEF1	ENST00000367220.9 linkuse as main transcript	c.321-29T>C		intron_variant		2	NM_001130700.2	ENSP00000356189.4		Q8WWN9-2
ENSG00000288520	ENST00000673182.1 linkuse as main transcript	c.1704-29T>C		intron_variant				ENSP00000499846.1

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25840

AN:

152052

Hom.:

2251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.0538

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.202

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.164

GnomAD3 exomes

AF:

0.158

AC:

39160

AN:

247458

Hom.:

3261

AF XY:

0.162

AC XY:

21656

AN XY:

133692

show subpopulations

Gnomad AFR exome

AF:

0.216

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.182

Gnomad EAS exome

AF:

0.189

Gnomad SAS exome

AF:

0.213

Gnomad FIN exome

AF:

0.126

Gnomad NFE exome

AF:

0.147

Gnomad OTH exome

AF:

0.159

GnomAD4 exome

AF:

0.155

AC:

222414

AN:

1431036

Hom.:

17947

Cov.:

AF XY:

0.158

AC XY:

112690

AN XY:

713662

show subpopulations

Gnomad4 AFR exome

AF:

0.220

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.184

Gnomad4 EAS exome

AF:

0.236

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.127

Gnomad4 NFE exome

AF:

0.148

Gnomad4 OTH exome

AF:

0.159

GnomAD4 genome

AF:

0.170

AC:

25851

AN:

152170

Hom.:

2251

Cov.:

AF XY:

0.169

AC XY:

12596

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.195

Gnomad4 EAS

AF:

0.202

Gnomad4 SAS

AF:

0.221

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.152

Gnomad4 OTH

AF:

0.162

Alfa

AF:

0.154

Hom.:

3865

Bravo

AF:

0.169

Asia WGS

AF:

0.209

AC:

727

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.9

DANN

Benign

0.83

BranchPoint Hunter

4.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over