rs13193677

Positions:

• chr6-154297800-G-A
• chr6-154297800-G-T

Variant summary

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

The NM_001130700.2(IPCEF1):​c.-61-8044C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,130 control chromosomes in the GnomAD database, including 796 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 0.095 (796 hom., cov: 32)
• Consequence: IPCEF1 NM_001130700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IPCEF1	NM_001130700.2	c.-61-8044C>T		intron_variant		ENST00000367220.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IPCEF1	ENST00000367220.9	c.-61-8044C>T		intron_variant		2	NM_001130700.2	A2
IPCEF1	ENST00000265198.8	c.-61-8044C>T		intron_variant		1		A2
IPCEF1	ENST00000422970.6	c.-61-8044C>T		intron_variant		1		A2
IPCEF1	ENST00000520261.1	c.-61-8044C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0954 AC: 14509 AN: 152012 Hom.: 797 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.0954 AC: 14507 AN: 152130 Hom.: 796 Cov.: 32 AF XY: 0.0955 AC XY: 7100 AN XY: 74366

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0873

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0824 Hom.: 748

Bravo AF: 0.0946

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.36

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: rs13193677; hg19: chr6-154618934;