rs13193677

Variant names:

• chr6-154297800-G-A
• rs13193677
• NM_001130700.2:c.-61-8044C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-154297800-G-A
• chr6-154297800-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.-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
• Publications: 2 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:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPCEF1	NM_001130700.2	MANE Select	c.-61-8044C>T		intron	N/A	NP_001124172.1	Q8WWN9-2
	IPCEF1	NM_001130699.2		c.-61-8044C>T		intron	N/A	NP_001124171.1	Q8WWN9-2
	IPCEF1	NM_001394799.1		c.-61-8044C>T		intron	N/A	NP_001381728.1	Q8WWN9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPCEF1	ENST00000367220.9	TSL:2 MANE Select	c.-61-8044C>T		intron	N/A	ENSP00000356189.4	Q8WWN9-2
	ENSG00000288520	ENST00000673182.1		c.1370-31836C>T		intron	N/A	ENSP00000499846.1
	IPCEF1	ENST00000422970.6	TSL:1	c.-61-8044C>T		intron	N/A	ENSP00000394751.2	Q8WWN9-2

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

African (AFR) AF: 0.129 AC: 5338 AN: 41472

American (AMR) AF: 0.0761 AC: 1163 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0845 AC: 293 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5174

South Asian (SAS) AF: 0.0439 AC: 212 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1277 AN: 10580

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5935 AN: 68004

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

Alfa AF: 0.0841 Hom.: 1095

Bravo AF: 0.0946

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.36
PhyloP100		0.37
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: rs13193677; hg19: chr6-154618934;