rs2768744

chr1-156902357-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PEAR1	NM_001080471.3	c.-9-1561G>A		intron_variant		ENST00000292357.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEAR1	ENST00000292357.8	c.-9-1561G>A		intron_variant		5	NM_001080471.3	P1
PEAR1	ENST00000338302.7	c.-10+72G>A		intron_variant		5		P1
PEAR1	ENST00000455314.5	c.-9-1561G>A		intron_variant		2
PEAR1	ENST00000444016.5	c.-9-1561G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88302 AN: 151918 Hom.: 30861 Cov.: 31

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.563

Gnomad4 FIN exome AF: 0.793

Gnomad4 NFE exome AF: 0.808

Gnomad4 OTH exome AF: 0.643

GnomAD4 genome AF: 0.581 AC: 88290 AN: 152036 Hom.: 30859 Cov.: 31 AF XY: 0.575 AC XY: 42750 AN XY: 74286

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.613

Alfa AF: 0.751 Hom.: 42773

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
Dann	Benign	0.39

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: rs2768744; hg19: chr1-156872149;