chr1-156907990-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001080471.3(PEAR1):c.841G>T(p.Gly281Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000942 in 1,574,882 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0050 ( 8 hom., cov: 32)
Exomes 𝑓: 0.00051 ( 6 hom. )
Consequence
PEAR1
NM_001080471.3 missense
NM_001080471.3 missense
Scores
2
9
6
Clinical Significance
Conservation
PhyloP100: 0.625
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0150509775).
BP6
?
Variant 1-156907990-G-T is Benign according to our data. Variant chr1-156907990-G-T is described in ClinVar as [Benign]. Clinvar id is 789552.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00498 (758/152224) while in subpopulation AFR AF= 0.0174 (722/41524). AF 95% confidence interval is 0.0163. There are 8 homozygotes in gnomad4. There are 342 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEAR1 | NM_001080471.3 | c.841G>T | p.Gly281Cys | missense_variant | 8/23 | ENST00000292357.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEAR1 | ENST00000292357.8 | c.841G>T | p.Gly281Cys | missense_variant | 8/23 | 5 | NM_001080471.3 | P1 | |
PEAR1 | ENST00000338302.7 | c.841G>T | p.Gly281Cys | missense_variant | 9/24 | 5 | P1 | ||
PEAR1 | ENST00000469390.5 | n.493G>T | non_coding_transcript_exon_variant | 4/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00498 AC: 758AN: 152106Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00115 AC: 212AN: 185056Hom.: 1 AF XY: 0.000767 AC XY: 76AN XY: 99082
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GnomAD4 exome AF: 0.000510 AC: 725AN: 1422658Hom.: 6 Cov.: 35 AF XY: 0.000460 AC XY: 324AN XY: 704136
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GnomAD4 genome ? AF: 0.00498 AC: 758AN: 152224Hom.: 8 Cov.: 32 AF XY: 0.00459 AC XY: 342AN XY: 74442
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Asia WGS
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H;H
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at