chr6-154304058-T-G

Variant names:

• chr6-154304058-T-G
• rs1534446
• NM_001130700.2:c.-61-14302A>C

Variant summary

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

The NM_001130700.2(IPCEF1):​c.-61-14302A>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
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 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.-61-14302A>C		intron	N/A	NP_001124172.1
	IPCEF1	NM_001130699.2		c.-62+2637A>C		intron	N/A	NP_001124171.1
	IPCEF1	NM_001394799.1		c.-62+2637A>C		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.-61-14302A>C		intron	N/A	ENSP00000356189.4
	ENSG00000288520	ENST00000673182.1		c.1370-38094A>C		intron	N/A	ENSP00000499846.1
	IPCEF1	ENST00000422970.6	TSL:1	c.-62+2637A>C		intron	N/A	ENSP00000394751.2

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

African (AFR) AF: 0.313 AC: 11657 AN: 37278

American (AMR) AF: 0.155 AC: 2344 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 344 AN: 3438

East Asian (EAS) AF: 0.335 AC: 1713 AN: 5118

South Asian (SAS) AF: 0.288 AC: 1362 AN: 4726

European-Finnish (FIN) AF: 0.0944 AC: 989 AN: 10480

Middle Eastern (MID) AF: 0.131 AC: 38 AN: 290

European-Non Finnish (NFE) AF: 0.0867 AC: 5881 AN: 67834

Other (OTH) AF: 0.141 AC: 294 AN: 2078

Alfa AF: 0.103 Hom.: 2622

Bravo AF: 0.170

Asia WGS AF: 0.265 AC: 924 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.5
DANN	Benign	0.51
PhyloP100		0.31
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: rs1534446; hg19: chr6-154625192;