dbSNP rs1051470: PEBP1:c.*624T>C (chr12-118145427-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002567.4(PEBP1):c.*624T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 161,264 control chromosomes in the GnomAD database, including 34,724 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 0.65 ( 32887 hom., cov: 31)

Exomes 𝑓: 0.62 ( 1837 hom. )

Consequence

PEBP1
NM_002567.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.102

Publications

19 publications found

Variant links:

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]

PEBP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEBP1	NM_002567.4 link	c.*624T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000261313.3	NP_002558.1	P30086D9IAI1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEBP1	ENST00000261313.3 link	c.*624T>C		3_prime_UTR_variant	Exon 4 of 4	1	NM_002567.4	ENSP00000261313.2		P30086

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

99318

AN:

151868

Hom.:

32843

Cov.:

show subpopulations

Gnomad AFR

AF:

0.726

Gnomad AMI

AF:

0.605

Gnomad AMR

AF:

0.678

Gnomad ASJ

AF:

0.622

Gnomad EAS

AF:

0.695

Gnomad SAS

AF:

0.747

Gnomad FIN

AF:

0.609

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.618

GnomAD4 exome

AF:

0.619

AC:

5746

AN:

9278

Hom.:

1837

Cov.:

AF XY:

0.628

AC XY:

3168

AN XY:

5044

show subpopulations

African (AFR)

AF:

0.778

AC:

AN:

American (AMR)

AF:

0.679

AC:

1183

AN:

1742

Ashkenazi Jewish (ASJ)

AF:

0.476

AC:

AN:

East Asian (EAS)

AF:

0.579

AC:

175

AN:

302

South Asian (SAS)

AF:

0.719

AC:

798

AN:

1110

European-Finnish (FIN)

AF:

0.585

AC:

AN:

164

Middle Eastern (MID)

AF:

0.333

AC:

AN:

European-Non Finnish (NFE)

AF:

0.586

AC:

3233

AN:

5520

Other (OTH)

AF:

0.606

AC:

223

AN:

368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

103

206

310

413

516

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

198

264

330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.654

AC:

99418

AN:

151986

Hom.:

32887

Cov.:

AF XY:

0.656

AC XY:

48739

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.726

AC:

30080

AN:

41450

American (AMR)

AF:

0.679

AC:

10362

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.622

AC:

2158

AN:

3472

East Asian (EAS)

AF:

0.695

AC:

3581

AN:

5150

South Asian (SAS)

AF:

0.746

AC:

3596

AN:

4818

European-Finnish (FIN)

AF:

0.609

AC:

6431

AN:

10554

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.606

AC:

41199

AN:

67960

Other (OTH)

AF:

0.617

AC:

1304

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1759

3517

5276

7034

8793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

806

1612

2418

3224

4030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.638

Hom.:

7469

Bravo

AF:

0.660

Asia WGS

AF:

0.691

AC:

2403

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.3

(source)

DANN

Benign

0.52

PhyloP100

-0.10

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over