chr7-101135963-C-T

Variant names:

• chr7-101135963-C-T
• rs2227692
• NM_000602.5:c.1087+162C>T

Variant summary

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

The NM_000602.5(SERPINE1):​c.1087+162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,226 control chromosomes in the GnomAD database, including 2,083 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 0.14 (2083 hom., cov: 32)
• Consequence: SERPINE1 NM_000602.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 21 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 Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000602.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINE1	NM_000602.5	MANE Select	c.1087+162C>T		intron	N/A	NP_000593.1
	SERPINE1	NM_001386460.1		c.1087+162C>T		intron	N/A	NP_001373389.1
	SERPINE1	NM_001386461.1		c.1087+162C>T		intron	N/A	NP_001373390.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINE1	ENST00000223095.5	TSL:1 MANE Select	c.1087+162C>T		intron	N/A	ENSP00000223095.4

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20929 AN: 152106 Hom.: 2074 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.138 AC: 20961 AN: 152226 Hom.: 2083 Cov.: 32 AF XY: 0.146 AC XY: 10886 AN XY: 74424

African (AFR) AF: 0.146 AC: 6056 AN: 41530

American (AMR) AF: 0.311 AC: 4757 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1789 AN: 5176

South Asian (SAS) AF: 0.216 AC: 1045 AN: 4830

European-Finnish (FIN) AF: 0.103 AC: 1097 AN: 10608

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0787 AC: 5355 AN: 68006

Other (OTH) AF: 0.162 AC: 343 AN: 2112

Alfa AF: 0.102 Hom.: 2604

Bravo AF: 0.152

Asia WGS AF: 0.297 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.38
DANN	Benign	0.58
PhyloP100		-2.6
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: rs2227692; hg19: chr7-100779244;