rs2936840

chr12-118141038-A-G

Variant summary

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

The NM_002567.4(PEBP1):c.346+1487A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,038 control chromosomes in the GnomAD database, including 45,124 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 0.77 (45124 hom., cov: 31)
• Consequence: PEBP1 NM_002567.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

PEBP1 (HGNC:8630): (phosphatidylethanolamine binding protein 1) This gene encodes a member of the phosphatidylethanolamine-binding family of proteins and has been shown to modulate multiple signaling pathways, including the MAP kinase (MAPK), NF-kappa B, and glycogen synthase kinase-3 (GSK-3) signaling pathways. The encoded protein can be further processed to form a smaller cleavage product, hippocampal cholinergic neurostimulating peptide (HCNP), which may be involved in neural development. This gene has been implicated in numerous human cancers and may act as a metastasis suppressor gene. Multiple pseudogenes of this gene have been identified in the genome. [provided by RefSeq, Jul 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PEBP1	NM_002567.4	c.346+1487A>G		intron_variant		ENST00000261313.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEBP1	ENST00000261313.3	c.346+1487A>G		intron_variant		1	NM_002567.4	P1
PEBP1	ENST00000542939.1	n.184+1487A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116239 AN: 151918 Hom.: 45081 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.765 AC: 116341 AN: 152038 Hom.: 45124 Cov.: 31 AF XY: 0.767 AC XY: 56975 AN XY: 74322

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.732

Alfa AF: 0.715 Hom.: 48287

Bravo AF: 0.778

Asia WGS AF: 0.819 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.70
Dann	Benign	0.32

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: rs2936840; hg19: chr12-118578843;