chr1-156915699-T-G

Variant names:

• chr1-156915699-T-G
• rs4661012
• NM_001080471.3:c.*901T>G

Variant summary

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

The NM_001080471.3(PEAR1):​c.*901T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,134 control chromosomes in the GnomAD database, including 10,455 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 0.36 (10455 hom., cov: 33)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: PEAR1 NM_001080471.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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.*901T>G		3_prime_UTR	Exon 23 of 23	NP_001073940.1	Q5VY43
	PEAR1	NM_001353682.2		c.*901T>G		3_prime_UTR	Exon 23 of 23	NP_001340611.1
	PEAR1	NM_001353683.2		c.*901T>G		3_prime_UTR	Exon 24 of 24	NP_001340612.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PEAR1	ENST00000292357.8	TSL:5 MANE Select	c.*901T>G		3_prime_UTR	Exon 23 of 23	ENSP00000292357.7	Q5VY43
	PEAR1	ENST00000971373.1		c.*901T>G		3_prime_UTR	Exon 25 of 25	ENSP00000641432.1
	PEAR1	ENST00000338302.7	TSL:5	c.*901T>G		3_prime_UTR	Exon 24 of 24	ENSP00000344465.3	Q5VY43

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55393 AN: 151992 Hom.: 10446 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.208 AC: 5 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.222 AC XY: 4 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.188 AC: 3 AN: 16

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.364 AC: 55423 AN: 152110 Hom.: 10455 Cov.: 33 AF XY: 0.369 AC XY: 27421 AN XY: 74340

African (AFR) AF: 0.294 AC: 12186 AN: 41496

American (AMR) AF: 0.455 AC: 6950 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1327 AN: 3472

East Asian (EAS) AF: 0.548 AC: 2834 AN: 5168

South Asian (SAS) AF: 0.538 AC: 2594 AN: 4822

European-Finnish (FIN) AF: 0.371 AC: 3922 AN: 10564

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24468 AN: 67988

Other (OTH) AF: 0.368 AC: 779 AN: 2114

Alfa AF: 0.362 Hom.: 6636

Bravo AF: 0.366

Asia WGS AF: 0.516 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.75
PhyloP100		0.45
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: rs4661012; hg19: chr1-156885491;