rs9322451

Variant names:

• chr6-154201527-G-A
• rs9322451
• NM_001130700.2:c.538-1487C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-154201527-G-A
• chr6-154201527-G-C
• chr6-154201527-G-T

Variant summary

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

The NM_001130700.2(IPCEF1):​c.538-1487C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,076 control chromosomes in the GnomAD database, including 4,803 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 0.23 (4803 hom., cov: 32)
• Consequence: IPCEF1 NM_001130700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 8 publications found

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]

ENSG00000288520 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130700.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPCEF1	NM_001130700.2	MANE Select	c.538-1487C>T		intron	N/A	NP_001124172.1
	IPCEF1	NM_001130699.2		c.538-1487C>T		intron	N/A	NP_001124171.1
	IPCEF1	NM_001394799.1		c.538-1487C>T		intron	N/A	NP_001381728.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPCEF1	ENST00000367220.9	TSL:2 MANE Select	c.538-1487C>T		intron	N/A	ENSP00000356189.4
	ENSG00000288520	ENST00000673182.1		c.1921-1487C>T		intron	N/A	ENSP00000499846.1
	IPCEF1	ENST00000422970.6	TSL:1	c.538-1487C>T		intron	N/A	ENSP00000394751.2

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35274 AN: 151956 Hom.: 4801 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.232 AC: 35293 AN: 152076 Hom.: 4803 Cov.: 32 AF XY: 0.241 AC XY: 17889 AN XY: 74340

African (AFR) AF: 0.263 AC: 10891 AN: 41484

American (AMR) AF: 0.157 AC: 2398 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3466

East Asian (EAS) AF: 0.610 AC: 3150 AN: 5166

South Asian (SAS) AF: 0.464 AC: 2238 AN: 4820

European-Finnish (FIN) AF: 0.275 AC: 2903 AN: 10550

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12654 AN: 67978

Other (OTH) AF: 0.225 AC: 476 AN: 2114

Alfa AF: 0.202 Hom.: 15284

Bravo AF: 0.220

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		0.15
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: rs9322451; hg19: chr6-154522661;