rs13268364

Positions:

• chr8-22849561-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_144962.3(PEBP4):​c.259-31826G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,214 control chromosomes in the GnomAD database, including 3,036 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 0.18 (3036 hom., cov: 32)
• Consequence: PEBP4 NM_144962.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PEBP4	NM_144962.3	c.259-31826G>A		intron_variant		ENST00000256404.8
PEBP4	NM_001363233.2	c.259-31826G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEBP4	ENST00000256404.8	c.259-31826G>A		intron_variant		1	NM_144962.3	P1
PEBP4	ENST00000521284.1	n.330-31826G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27133 AN: 152096 Hom.: 3039 Cov.: 32

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.178 AC: 27121 AN: 152214 Hom.: 3036 Cov.: 32 AF XY: 0.174 AC XY: 12933 AN XY: 74400

Gnomad4 AFR AF: 0.0523

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.0905

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.197

Alfa AF: 0.244 Hom.: 6410

Bravo AF: 0.174

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	15
DANN	Benign	0.78

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: rs13268364; hg19: chr8-22707074;