6-154304058-T-G

Position:

• chr6-154304058-T-G

Variant summary

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

The NM_001130700.2(IPCEF1):​c.-61-14302A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 147,296 control chromosomes in the GnomAD database, including 2,656 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 0.17 (2656 hom., cov: 31)
• Consequence: IPCEF1 NM_001130700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IPCEF1	NM_001130700.2	c.-61-14302A>C		intron_variant		ENST00000367220.9	NP_001124172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IPCEF1	ENST00000367220.9	c.-61-14302A>C		intron_variant		2	NM_001130700.2	ENSP00000356189	A2
IPCEF1	ENST00000265198.8	c.-61-14302A>C		intron_variant		1		ENSP00000265198	A2
IPCEF1	ENST00000422970.6	c.-62+2637A>C		intron_variant		1		ENSP00000394751	A2
IPCEF1	ENST00000520261.1	c.-62+2637A>C		intron_variant		4		ENSP00000431004

Frequencies

GnomAD3 genomes AF: 0.168 AC: 24662 AN: 147182 Hom.: 2638 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.168 AC: 24718 AN: 147296 Hom.: 2656 Cov.: 31 AF XY: 0.172 AC XY: 12349 AN XY: 71910

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.0867

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0937 Hom.: 1477

Bravo AF: 0.170

Asia WGS AF: 0.265 AC: 924 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.5
DANN	Benign	0.51

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: rs1534446; hg19: chr6-154625192;