dbSNP rs57731889: PEAR1:c.2081-25C>T (chr1-156912469-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001080471.3(PEAR1):c.2081-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,607,396 control chromosomes in the GnomAD database, including 15,286 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 0.12 ( 1805 hom., cov: 32)

Exomes 𝑓: 0.10 ( 13481 hom. )

Consequence

PEAR1
NM_001080471.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0860

Publications

18 publications found

Variant links:

Genes affected

PEAR1 (HGNC:33631): (platelet endothelial aggregation receptor 1) PEAR1 is a platelet receptor that signals upon the formation of platelet-platelet contacts independent of platelet activation and secondary to platelet aggregation (Nanda et al., 2005 [PubMed 15851471]).[supplied by OMIM, Mar 2008]

PEAR1 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEAR1	NM_001080471.3 link	c.2081-25C>T		intron_variant	Intron 16 of 22	ENST00000292357.8	NP_001073940.1	Q5VY43

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PEAR1	ENST00000292357.8 link	c.2081-25C>T	intron_variant	Intron 16 of 22	5	NM_001080471.3	ENSP00000292357.7	Q5VY43
PEAR1	ENST00000338302.7 link	c.2081-25C>T	intron_variant	Intron 17 of 23	5		ENSP00000344465.3	Q5VY43
PEAR1	ENST00000469390.5 link	n.1809-25C>T	intron_variant	Intron 11 of 17	2

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18973

AN:

152108

Hom.:

1797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.0724

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.0709

Gnomad EAS

AF:

0.447

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.0565

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0719

Gnomad OTH

AF:

0.125

GnomAD2 exomes

AF:

0.166

AC:

40898

AN:

245812

AF XY:

0.161

show subpopulations

Gnomad AFR exome

AF:

0.141

Gnomad AMR exome

AF:

0.352

Gnomad ASJ exome

AF:

0.0745

Gnomad EAS exome

AF:

0.469

Gnomad FIN exome

AF:

0.0536

Gnomad NFE exome

AF:

0.0723

Gnomad OTH exome

AF:

0.131

GnomAD4 exome

AF:

0.101

AC:

147235

AN:

1455170

Hom.:

13481

Cov.:

AF XY:

0.105

AC XY:

75666

AN XY:

723400

show subpopulations

African (AFR)

AF:

0.140

AC:

4636

AN:

33166

American (AMR)

AF:

0.336

AC:

14698

AN:

43724

Ashkenazi Jewish (ASJ)

AF:

0.0728

AC:

1870

AN:

25672

East Asian (EAS)

AF:

0.449

AC:

17768

AN:

39614

South Asian (SAS)

AF:

0.250

AC:

21381

AN:

85368

European-Finnish (FIN)

AF:

0.0541

AC:

2871

AN:

53064

Middle Eastern (MID)

AF:

0.0925

AC:

529

AN:

5720

European-Non Finnish (NFE)

AF:

0.0690

AC:

76489

AN:

1108796

Other (OTH)

AF:

0.116

AC:

6993

AN:

60046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

6859

13718

20576

27435

34294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3298

6596

9894

13192

16490

<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:

0.125

AC:

18998

AN:

152226

Hom.:

1805

Cov.:

AF XY:

0.130

AC XY:

9661

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.138

AC:

5747

AN:

41524

American (AMR)

AF:

0.232

AC:

3549

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0709

AC:

246

AN:

3472

East Asian (EAS)

AF:

0.447

AC:

2308

AN:

5160

South Asian (SAS)

AF:

0.270

AC:

1300

AN:

4816

European-Finnish (FIN)

AF:

0.0565

AC:

600

AN:

10620

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0718

AC:

4885

AN:

68012

Other (OTH)

AF:

0.129

AC:

273

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

772

1544

2316

3088

3860

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.0930

Hom.:

256

Bravo

AF:

0.137

Asia WGS

AF:

0.365

AC:

1268

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.7

(source)

DANN

Benign

0.43

PhyloP100

0.086

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

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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