NM_144962.3:c.358-25037A>C

Variant names:

• chr8-22752257-T-G
• rs4872550
• NM_144962.3:c.358-25037A>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.358-25037A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,118 control chromosomes in the GnomAD database, including 60,744 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 0.89 (60744 hom., cov: 31)
• Consequence: PEBP4 NM_144962.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 2 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]

LOC107986925 (HGNC:):

EGR3-AS1 (HGNC:58186):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144962.3. 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
	PEBP4	NM_144962.3	MANE Select	c.358-25037A>C		intron	N/A	NP_659399.2	Q96S96
	PEBP4	NM_001363233.2		c.358-25037A>C		intron	N/A	NP_001350162.1	Q96S96

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PEBP4	ENST00000256404.8	TSL:1 MANE Select	c.358-25037A>C		intron	N/A	ENSP00000256404.6	Q96S96
	PEBP4	ENST00000901323.1		c.358-25037A>C		intron	N/A	ENSP00000571382.1
	PEBP4	ENST00000901324.1		c.358-25037A>C		intron	N/A	ENSP00000571383.1

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135184 AN: 152000 Hom.: 60689 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.889 AC: 135296 AN: 152118 Hom.: 60744 Cov.: 31 AF XY: 0.891 AC XY: 66226 AN XY: 74362

African (AFR) AF: 0.747 AC: 30931 AN: 41410

American (AMR) AF: 0.944 AC: 14447 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3316 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5183 AN: 5188

South Asian (SAS) AF: 0.957 AC: 4609 AN: 4814

European-Finnish (FIN) AF: 0.930 AC: 9855 AN: 10594

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.939 AC: 63889 AN: 68022

Other (OTH) AF: 0.907 AC: 1914 AN: 2110

Alfa AF: 0.932 Hom.: 33640

Bravo AF: 0.884

Asia WGS AF: 0.971 AC: 3377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.81
PhyloP100		-0.13
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: rs4872550; hg19: chr8-22609770;