dbSNP rs2768744: PEAR1:c.-9-1561G>A (chr1-156902357-G-A) – 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.-9-1561G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,812 control chromosomes in the GnomAD database, including 31,097 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 0.58 ( 30859 hom., cov: 31)

Exomes 𝑓: 0.77 ( 238 hom. )

Consequence

PEAR1
NM_001080471.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.220

Publications

9 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEAR1	NM_001080471.3 link	c.-9-1561G>A		intron_variant	Intron 1 of 22	ENST00000292357.8	NP_001073940.1	Q5VY43

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PEAR1	ENST00000292357.8 link	c.-9-1561G>A	intron_variant	Intron 1 of 22	5	NM_001080471.3	ENSP00000292357.7	Q5VY43
PEAR1	ENST00000338302.7 link	c.-10+72G>A	intron_variant	Intron 2 of 23	5		ENSP00000344465.3	Q5VY43
PEAR1	ENST00000455314.5 link	c.-9-1561G>A	intron_variant	Intron 1 of 5	2		ENSP00000389742.1	A6PVP2
PEAR1	ENST00000444016.5 link	n.-9-1561G>A	intron_variant	Intron 1 of 6	3		ENSP00000397870.1	F2Z2F7

Frequencies

GnomAD3 genomes

AF:

0.581

AC:

88302

AN:

151918

Hom.:

30861

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.783

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.752

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.797

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.794

Gnomad OTH

AF:

0.618

GnomAD4 exome

AF:

0.774

AC:

601

AN:

776

Hom.:

238

AF XY:

0.760

AC XY:

389

AN XY:

512

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.667

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.563

AC:

AN:

European-Finnish (FIN)

AF:

0.793

AC:

214

AN:

270

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.808

AC:

354

AN:

438

Other (OTH)

AF:

0.643

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.581

AC:

88290

AN:

152036

Hom.:

30859

Cov.:

AF XY:

0.575

AC XY:

42750

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.209

AC:

8678

AN:

41482

American (AMR)

AF:

0.612

AC:

9352

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.752

AC:

2607

AN:

3468

East Asian (EAS)

AF:

0.194

AC:

1002

AN:

5164

South Asian (SAS)

AF:

0.428

AC:

2061

AN:

4810

European-Finnish (FIN)

AF:

0.797

AC:

8420

AN:

10564

Middle Eastern (MID)

AF:

0.714

AC:

210

AN:

294

European-Non Finnish (NFE)

AF:

0.794

AC:

53953

AN:

67958

Other (OTH)

AF:

0.613

AC:

1293

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1352

2704

4057

5409

6761

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

690

1380

2070

2760

3450

<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:

0.695

Hom.:

67561

Bravo

AF:

0.557

Asia WGS

AF:

0.296

AC:

1030

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.69

(source)

DANN

Benign

0.39

PhyloP100

0.22

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