NM_144962.3:c.358-12581T>C

Variant names:

• chr8-22739801-A-G
• rs7013424
• NM_144962.3:c.358-12581T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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:58186):

LOC124901908 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PEBP4	NM_144962.3	c.358-12581T>C		intron_variant	Intron 4 of 6	ENST00000256404.8	NP_659399.2
PEBP4	NM_001363233.2	c.358-12581T>C		intron_variant	Intron 4 of 6		NP_001350162.1
LOC124901908	XR_007060855.1	n.381+54A>G		intron_variant	Intron 1 of 2
LOC124901908	XR_007060856.1	n.381+54A>G		intron_variant	Intron 1 of 2

Ensembl

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

African (AFR) AF: 0.441 AC: 18262 AN: 41402

American (AMR) AF: 0.349 AC: 5321 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3472

East Asian (EAS) AF: 0.0732 AC: 378 AN: 5162

South Asian (SAS) AF: 0.152 AC: 728 AN: 4802

European-Finnish (FIN) AF: 0.270 AC: 2851 AN: 10548

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17385 AN: 67960

Other (OTH) AF: 0.285 AC: 600 AN: 2108

Alfa AF: 0.285 Hom.: 7857

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
PhyloP100		-0.41
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: rs7013424; hg19: chr8-22597314;