rs2227692

Positions:

• chr7-101135963-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINE1	NM_000602.5	c.1087+162C>T		intron_variant		ENST00000223095.5	NP_000593.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINE1	ENST00000223095.5	c.1087+162C>T		intron_variant		1	NM_000602.5	ENSP00000223095	P1

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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0787

Gnomad4 OTH AF: 0.162

Alfa AF: 0.103 Hom.: 1045

Bravo AF: 0.152

Asia WGS AF: 0.297 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.38
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227692; hg19: chr7-100779244;