chr10-73911598-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002658.6(PLAU):c.43G>T(p.Val15Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0086 in 1,613,832 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0076 ( 16 hom., cov: 32)
Exomes 𝑓: 0.0087 ( 123 hom. )
Consequence
PLAU
NM_002658.6 missense
NM_002658.6 missense
Scores
1
12
Clinical Significance
Conservation
PhyloP100: 0.995
Genes affected
PLAU (HGNC:9052): (plasminogen activator, urokinase) This gene encodes a secreted serine protease that converts plasminogen to plasmin. The encoded preproprotein is proteolytically processed to generate A and B polypeptide chains. These chains associate via a single disulfide bond to form the catalytically inactive high molecular weight urokinase-type plasminogen activator (HMW-uPA). HMW-uPA can be further processed into the catalytically active low molecular weight urokinase-type plasminogen activator (LMW-uPA). This low molecular weight form does not bind to the urokinase-type plasminogen activator receptor. Mutations in this gene may be associated with Quebec platelet disorder and late-onset Alzheimer's disease. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Jan 2016]
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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=0.0038291514).
BP6
?
Variant 10-73911598-G-T is Benign according to our data. Variant chr10-73911598-G-T is described in ClinVar as [Benign]. Clinvar id is 300740.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-73911598-G-T is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00765 (1165/152338) while in subpopulation SAS AF= 0.0236 (114/4828). AF 95% confidence interval is 0.0201. There are 16 homozygotes in gnomad4. There are 551 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1169 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLAU | NM_002658.6 | c.43G>T | p.Val15Leu | missense_variant | 2/11 | ENST00000372764.4 | |
C10orf55 | NR_160938.1 | n.884C>A | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLAU | ENST00000372764.4 | c.43G>T | p.Val15Leu | missense_variant | 2/11 | 1 | NM_002658.6 | P1 | |
C10orf55 | ENST00000409178.5 | n.884C>A | non_coding_transcript_exon_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00768 AC: 1169AN: 152220Hom.: 17 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0105 AC: 2609AN: 249498Hom.: 27 AF XY: 0.0120 AC XY: 1616AN XY: 135156
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GnomAD4 exome AF: 0.00870 AC: 12712AN: 1461494Hom.: 123 Cov.: 32 AF XY: 0.00968 AC XY: 7035AN XY: 727022
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GnomAD4 genome ? AF: 0.00765 AC: 1165AN: 152338Hom.: 16 Cov.: 32 AF XY: 0.00740 AC XY: 551AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Quebec platelet disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Benign
T
Sift4G
Pathogenic
D;T
Vest4
0.051
MutPred
Loss of sheet (P = 0.0181);Loss of sheet (P = 0.0181);
MPC
0.28
ClinPred
T
GERP RS
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