rs2936840

Variant names:

• chr12-118141038-A-G
• rs2936840
• NM_002567.4:c.346+1487A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-118141038-A-G
• chr12-118141038-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PEBP1	NM_002567.4	c.346+1487A>G		intron_variant	Intron 3 of 3	ENST00000261313.3	NP_002558.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEBP1	ENST00000261313.3	c.346+1487A>G		intron_variant	Intron 3 of 3	1	NM_002567.4	ENSP00000261313.2
PEBP1	ENST00000542939.1	n.184+1487A>G		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.874 AC: 36261 AN: 41496

American (AMR) AF: 0.786 AC: 12014 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3468

East Asian (EAS) AF: 0.922 AC: 4769 AN: 5172

South Asian (SAS) AF: 0.775 AC: 3738 AN: 4824

European-Finnish (FIN) AF: 0.690 AC: 7282 AN: 10554

Middle Eastern (MID) AF: 0.634 AC: 184 AN: 290

European-Non Finnish (NFE) AF: 0.700 AC: 47530 AN: 67942

Other (OTH) AF: 0.732 AC: 1544 AN: 2108

Alfa AF: 0.722 Hom.: 63293

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
PhyloP100		-0.29
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: rs2936840; hg19: chr12-118578843;