chr1-156899056-T-C

Variant names:

• chr1-156899056-T-C
• rs12407092
• NM_001080471.3:c.-9-4862T>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.-9-4862T>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
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080471.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PEAR1	NM_001080471.3	MANE Select	c.-9-4862T>C		intron	N/A	NP_001073940.1	Q5VY43
	PEAR1	NM_001353682.2		c.-347-4862T>C		intron	N/A	NP_001340611.1
	PEAR1	NM_001353683.2		c.-506-3132T>C		intron	N/A	NP_001340612.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PEAR1	ENST00000292357.8	TSL:5 MANE Select	c.-9-4862T>C		intron	N/A	ENSP00000292357.7	Q5VY43
	PEAR1	ENST00000971373.1		c.-178-3132T>C		intron	N/A	ENSP00000641432.1
	PEAR1	ENST00000338302.7	TSL:5	c.-107-3132T>C		intron	N/A	ENSP00000344465.3	Q5VY43

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

African (AFR) AF: 0.0988 AC: 4105 AN: 41534

American (AMR) AF: 0.153 AC: 2346 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1809 AN: 5180

South Asian (SAS) AF: 0.200 AC: 963 AN: 4816

European-Finnish (FIN) AF: 0.132 AC: 1398 AN: 10578

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.109 AC: 7413 AN: 67998

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.109 Hom.: 204

Bravo AF: 0.125

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.27
DANN	Benign	0.64
PhyloP100		-1.5
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: rs12407092; hg19: chr1-156868848;