1-156899056-T-C

Position:

• chr1-156899056-T-C

Variant summary

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

The NM_001080471.3(PEAR1):​c.-9-4862T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,184 control chromosomes in the GnomAD database, including 1,355 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 (1355 hom., cov: 32)
• Consequence: PEAR1 NM_001080471.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PEAR1	NM_001080471.3	c.-9-4862T>C		intron_variant		ENST00000292357.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEAR1	ENST00000292357.8	c.-9-4862T>C		intron_variant		5	NM_001080471.3	P1
PEAR1	ENST00000338302.7	c.-107-3132T>C		intron_variant		5		P1
PEAR1	ENST00000455314.5	c.-9-4862T>C		intron_variant		2
PEAR1	ENST00000444016.5	c.-9-4862T>C		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18894 AN: 152066 Hom.: 1352 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.124 AC: 18904 AN: 152184 Hom.: 1355 Cov.: 32 AF XY: 0.129 AC XY: 9628 AN XY: 74394

Gnomad4 AFR AF: 0.0988

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.126

Alfa AF: 0.108 Hom.: 198

Bravo AF: 0.125

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.27
DANN	Benign	0.64

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: rs12407092; hg19: chr1-156868848;