6-160733923-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000301.5(PLG):c.1588-72C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 769,686 control chromosomes in the GnomAD database, including 4,769 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 2920 hom., cov: 30)
Exomes 𝑓: 0.041 ( 1849 hom. )
Consequence
PLG
NM_000301.5 intron
NM_000301.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.04
Publications
5 publications found
Genes affected
PLG (HGNC:9071): (plasminogen) The plasminogen protein encoded by this gene is a serine protease that circulates in blood plasma as an inactive zymogen and is converted to the active protease, plasmin, by several plasminogen activators such as tissue plasminogen activator (tPA), urokinase plasminogen activator (uPA), kallikrein, and factor XII (Hageman factor). The conversion of plasminogen to plasmin involves the cleavage of the peptide bond between Arg-561 and Val-562. Plasmin cleavage also releases the angiostatin protein which inhibits angiogenesis. Plasmin degrades many blood plasma proteins, including fibrin-containing blood clots. As a serine protease, plasmin cleaves many products in addition to fibrin such as fibronectin, thrombospondin, laminin, and von Willebrand factor. Plasmin is inactivated by proteins such as alpha-2-macroglobulin and alpha-2-antiplasmin in addition to inhibitors of the various plasminogen activators. Plasminogen also interacts with plasminogen receptors which results in the retention of plasmin on cell surfaces and in plasmin-induced cell signaling. The localization of plasminogen on cell surfaces plays a role in the degradation of extracellular matrices, cell migration, inflamation, wound healing, oncogenesis, metastasis, myogenesis, muscle regeneration, neurite outgrowth, and fibrinolysis. This protein may also play a role in acute respiratory distress syndrome (ARDS) which, in part, is caused by enhanced clot formation and the suppression of fibrinolysis. Compared to other mammals, the cluster of plasminogen-like genes to which this gene belongs has been rearranged in catarrhine primates. [provided by RefSeq, May 2020]
PLG Gene-Disease associations (from GenCC):
- hypoplasminogenemiaInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- angioedema, hereditary, 4Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
Variant 6-160733923-C-T is Benign according to our data. Variant chr6-160733923-C-T is described in ClinVar as [Benign]. Clinvar id is 1265723.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.125 AC: 18890AN: 150818Hom.: 2913 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
18890
AN:
150818
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0414 AC: 25625AN: 618762Hom.: 1849 AF XY: 0.0400 AC XY: 13494AN XY: 337180 show subpopulations
GnomAD4 exome
AF:
AC:
25625
AN:
618762
Hom.:
AF XY:
AC XY:
13494
AN XY:
337180
show subpopulations
African (AFR)
AF:
AC:
6376
AN:
17076
American (AMR)
AF:
AC:
1885
AN:
41930
Ashkenazi Jewish (ASJ)
AF:
AC:
1650
AN:
19422
East Asian (EAS)
AF:
AC:
9
AN:
34090
South Asian (SAS)
AF:
AC:
3099
AN:
69632
European-Finnish (FIN)
AF:
AC:
807
AN:
50322
Middle Eastern (MID)
AF:
AC:
682
AN:
3952
European-Non Finnish (NFE)
AF:
AC:
9023
AN:
350960
Other (OTH)
AF:
AC:
2094
AN:
31378
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.520
Heterozygous variant carriers
0
1197
2393
3590
4786
5983
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.125 AC: 18933AN: 150924Hom.: 2920 Cov.: 30 AF XY: 0.122 AC XY: 8963AN XY: 73664 show subpopulations
GnomAD4 genome
AF:
AC:
18933
AN:
150924
Hom.:
Cov.:
30
AF XY:
AC XY:
8963
AN XY:
73664
show subpopulations
African (AFR)
AF:
AC:
15031
AN:
40882
American (AMR)
AF:
AC:
1040
AN:
15198
Ashkenazi Jewish (ASJ)
AF:
AC:
281
AN:
3452
East Asian (EAS)
AF:
AC:
5
AN:
5156
South Asian (SAS)
AF:
AC:
224
AN:
4792
European-Finnish (FIN)
AF:
AC:
198
AN:
10360
Middle Eastern (MID)
AF:
AC:
82
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1825
AN:
67788
Other (OTH)
AF:
AC:
246
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.512
Heterozygous variant carriers
0
621
1242
1864
2485
3106
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
157
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 20, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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