1-156903671-T-C

Variant names:

• chr1-156903671-T-C
• rs11264579
• NM_001080471.3:c.-9-247T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080471.3(PEAR1):​c.-9-247T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,040 control chromosomes in the GnomAD database, including 15,033 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 0.39 (15033 hom., cov: 32)
• Consequence: PEAR1 NM_001080471.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 10 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEAR1	NM_001080471.3	c.-9-247T>C		intron_variant	Intron 1 of 22	ENST00000292357.8	NP_001073940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEAR1	ENST00000292357.8	c.-9-247T>C		intron_variant	Intron 1 of 22	5	NM_001080471.3	ENSP00000292357.7
PEAR1	ENST00000338302.7	c.-9-247T>C		intron_variant	Intron 2 of 23	5		ENSP00000344465.3
PEAR1	ENST00000455314.5	c.-9-247T>C		intron_variant	Intron 1 of 5	2		ENSP00000389742.1
PEAR1	ENST00000444016.5	n.-9-247T>C		intron_variant	Intron 1 of 6	3		ENSP00000397870.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58614 AN: 151922 Hom.: 14982 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.359

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.386 AC: 58725 AN: 152040 Hom.: 15033 Cov.: 32 AF XY: 0.392 AC XY: 29143 AN XY: 74316

African (AFR) AF: 0.677 AC: 28052 AN: 41428

American (AMR) AF: 0.376 AC: 5750 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 866 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4108 AN: 5156

South Asian (SAS) AF: 0.572 AC: 2756 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2143 AN: 10576

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13994 AN: 67988

Other (OTH) AF: 0.364 AC: 771 AN: 2116

Alfa AF: 0.261 Hom.: 20171

Bravo AF: 0.407

Asia WGS AF: 0.696 AC: 2420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.072
DANN	Benign	0.25
PhyloP100		-1.8
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: rs11264579; hg19: chr1-156873463;