rs9322453

chr6-154247041-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001130700.2(IPCEF1):c.77-281C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 409,484 control chromosomes in the GnomAD database, including 30,483 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 0.36 (10478 hom., cov: 31)
  • Exomes 𝑓: 0.38 (20005 hom.)
• Consequence: IPCEF1 NM_001130700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• 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/exons	MANE	UniProt
IPCEF1	NM_001130700.2	c.77-281C>G		intron_variant		ENST00000367220.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IPCEF1	ENST00000367220.9	c.77-281C>G		intron_variant		2	NM_001130700.2	A2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55244 AN: 151544 Hom.: 10481 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.381

GnomAD4 exome AF: 0.383 AC: 98847 AN: 257838 Hom.: 20005 Cov.: 4 AF XY: 0.381 AC XY: 50377 AN XY: 132136

Gnomad4 AFR exome AF: 0.291

Gnomad4 AMR exome AF: 0.259

Gnomad4 ASJ exome AF: 0.529

Gnomad4 EAS exome AF: 0.249

Gnomad4 SAS exome AF: 0.214

Gnomad4 FIN exome AF: 0.416

Gnomad4 NFE exome AF: 0.415

Gnomad4 OTH exome AF: 0.390

GnomAD4 genome AF: 0.364 AC: 55250 AN: 151646 Hom.: 10478 Cov.: 31 AF XY: 0.361 AC XY: 26728 AN XY: 74084

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.380

Alfa AF: 0.383 Hom.: 1474

Bravo AF: 0.359

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	11
Dann	Benign	0.80

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

Other links and lift over

dbSNP: rs9322453; hg19: chr6-154568175; COSMIC: COSV54550625; COSMIC: COSV54550625;