rs7013424

Positions:

• chr8-22739801-A-G

Variant summary

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

The NM_144962.3(PEBP4):​c.358-12581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,918 control chromosomes in the GnomAD database, including 7,985 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 0.31 (7985 hom., cov: 32)
• Consequence: PEBP4 NM_144962.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

Genes affected

PEBP4 (HGNC:28319): (phosphatidylethanolamine binding protein 4) The phosphatidylethanolamine (PE)-binding proteins, including PEBP4, are an evolutionarily conserved family of proteins with pivotal biologic functions, such as lipid binding and inhibition of serine proteases (Wang et al., 2004 [PubMed 15302887]).[supplied by OMIM, Dec 2008]

ENSG00000253125 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PEBP4	NM_144962.3	c.358-12581T>C		intron_variant		ENST00000256404.8	NP_659399.2
PEBP4	NM_001363233.2	c.358-12581T>C		intron_variant			NP_001350162.1
LOC124901908	XR_007060855.1	n.381+54A>G		intron_variant
LOC124901908	XR_007060856.1	n.381+54A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PEBP4	ENST00000256404.8	c.358-12581T>C		intron_variant		1	NM_144962.3	ENSP00000256404.6
ENSG00000253125	ENST00000523627.1	n.165-4793A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46978 AN: 151798 Hom.: 7965 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.0731

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.310 AC: 47047 AN: 151918 Hom.: 7985 Cov.: 32 AF XY: 0.308 AC XY: 22884 AN XY: 74260

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.0732

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.285

Alfa AF: 0.273 Hom.: 4835

Bravo AF: 0.321

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.37
DANN	Benign	0.61

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: rs7013424; hg19: chr8-22597314;