Variant rs34078713 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001136528.2(SERPINE2):c.191T>C(p.Met64Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00834 in 1,614,172 control chromosomes in the GnomAD database, including 70 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 0.0075 ( 10 hom., cov: 32)

Exomes 𝑓: 0.0084 ( 60 hom. )

Consequence

SERPINE2
NM_001136528.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 8.37

Variant links:

Genes affected

SERPINE2 (HGNC:8951): (serpin family E member 2) This gene encodes a member of the serpin family of proteins, a group of proteins that inhibit serine proteases. Thrombin, urokinase, plasmin and trypsin are among the proteases that this family member can inhibit. This gene is a susceptibility gene for chronic obstructive pulmonary disease and for emphysema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

SERPINE2 links:

SERPINE2 (HGNC:):

SERPINE2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.017178237).

BS2

High AC in GnomAd4 at 1144 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINE2	NM_001136528.2 linkuse as main transcript	c.191T>C	p.Met64Thr	missense_variant	2/9	ENST00000409304.6	NP_001130000.1	P07093-2A0A024R498

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINE2	ENST00000409304.6 linkuse as main transcript	c.191T>C	p.Met64Thr	missense_variant	2/9	1	NM_001136528.2	ENSP00000386412.1		P07093-2

Frequencies

GnomAD3 genomes

AF:

0.00752

AC:

1144

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00169

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.0113

Gnomad ASJ

AF:

0.00806

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.0108

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00750

AC:

1883

AN:

251216

Hom.:

AF XY:

0.00780

AC XY:

1059

AN XY:

135762

show subpopulations

Gnomad AFR exome

AF:

0.00160

Gnomad AMR exome

AF:

0.00717

Gnomad ASJ exome

AF:

0.00824

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000719

Gnomad FIN exome

AF:

0.0103

Gnomad NFE exome

AF:

0.0108

Gnomad OTH exome

AF:

0.00849

GnomAD4 exome

AF:

0.00843

AC:

12318

AN:

1461868

Hom.:

Cov.:

AF XY:

0.00829

AC XY:

6032

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00102

Gnomad4 AMR exome

AF:

0.00709

Gnomad4 ASJ exome

AF:

0.00761

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000707

Gnomad4 FIN exome

AF:

0.0111

Gnomad4 NFE exome

AF:

0.00958

Gnomad4 OTH exome

AF:

0.00720

GnomAD4 genome

AF:

0.00751

AC:

1144

AN:

152304

Hom.:

Cov.:

AF XY:

0.00760

AC XY:

566

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00168

Gnomad4 AMR

AF:

0.0113

Gnomad4 ASJ

AF:

0.00806

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.0108

Gnomad4 NFE

AF:

0.0102

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.00911

Hom.:

Bravo

AF:

0.00721

TwinsUK

AF:

0.00944

AC:

ALSPAC

AF:

0.00934

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.0109

AC:

ExAC

AF:

0.00751

AC:

912

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00829

EpiControl

AF:

0.0122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.79

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Uncertain

0.030

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Pathogenic

0.86

.;D;.;.;T;T

Eigen

Pathogenic

0.79

Eigen_PC

Pathogenic

0.77

FATHMM_MKL

Pathogenic

1.0

LIST_S2

Uncertain

0.88

.;D;D;D;D;D

MetaRNN

Benign

0.017

T;T;T;T;T;T

MetaSVM

Uncertain

0.37

MutationAssessor

Pathogenic

3.5

H;H;H;.;.;.

PrimateAI

Uncertain

0.57

PROVEAN

Pathogenic

-4.6

D;D;D;D;D;D

REVEL

Pathogenic

0.85

Sift

Uncertain

0.0020

D;D;D;D;D;D

Sift4G

Uncertain

0.0060

D;D;D;D;.;.

Polyphen

0.93

.;P;.;.;.;.

Vest4

0.55

MVP

0.68

MPC

0.89

ClinPred

0.038

GERP RS

5.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.85

gMVP

0.94

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over