rs34857375

Variant names:

• chr7-101126425-T-TG
• rs1799762
• ENST00000950058.1:c.-123+152_-123+153insG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000950058.1(SERPINE1):​c.-123+152_-123+153insG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24951 hom., cov: 0)
• Consequence: SERPINE1 ENST00000950058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 20 publications found

Genes affected

SERPINE1 (HGNC:8583): (serpin family E member 1) This gene encodes a member of the serine proteinase inhibitor (serpin) superfamily. This member is the principal inhibitor of tissue plasminogen activator (tPA) and urokinase (uPA), and hence is an inhibitor of fibrinolysis. The protein also functions as a component of innate antiviral immunity. Defects in this gene are the cause of plasminogen activator inhibitor-1 deficiency (PAI-1 deficiency), and high concentrations of the gene product are associated with thrombophilia. [provided by RefSeq, Aug 2020]

SERPINE1 Gene-Disease associations (from GenCC):

• congenital plasminogen activator inhibitor type 1 deficiency

  Inheritance: AR, SD Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000950058.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINE1	ENST00000950058.1		c.-123+152_-123+153insG		intron	N/A	ENSP00000620117.1

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84640 AN: 151736 Hom.: 24889 Cov.: 0

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.578

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.558 AC: 84764 AN: 151852 Hom.: 24951 Cov.: 0 AF XY: 0.560 AC XY: 41547 AN XY: 74196

African (AFR) AF: 0.739 AC: 30639 AN: 41474

American (AMR) AF: 0.635 AC: 9694 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2176 AN: 5144

South Asian (SAS) AF: 0.498 AC: 2333 AN: 4686

European-Finnish (FIN) AF: 0.491 AC: 5187 AN: 10564

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31335 AN: 67944

Other (OTH) AF: 0.581 AC: 1225 AN: 2110

Alfa AF: 0.515 Hom.: 2577

Bravo AF: 0.574

Asia WGS AF: 0.531 AC: 1834 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1799762; hg19: chr7-100769706;