Variant 2-223980202-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001136528.2(SERPINE2):c.1072+109G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 886,048 control chromosomes in the GnomAD database, including 273,195 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 0.77 ( 45299 hom., cov: 33)

Exomes 𝑓: 0.78 ( 227896 hom. )

Consequence

SERPINE2
NM_001136528.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINE2	NM_001136528.2 link	c.1072+109G>C		intron_variant		ENST00000409304.6	NP_001130000.1	P07093-2A0A024R498

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINE2	ENST00000409304.6 link	c.1072+109G>C		intron_variant		1	NM_001136528.2	ENSP00000386412.1		P07093-2

Frequencies

GnomAD3 genomes

AF:

0.767

AC:

116644

AN:

152056

Hom.:

45274

Cov.:

show subpopulations

Gnomad AFR

AF:

0.713

Gnomad AMI

AF:

0.900

Gnomad AMR

AF:

0.808

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.445

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.790

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.820

Gnomad OTH

AF:

0.766

GnomAD4 exome

AF:

0.782

AC:

574194

AN:

733874

Hom.:

227896

Cov.:

AF XY:

0.777

AC XY:

299220

AN XY:

385142

show subpopulations

Gnomad4 AFR exome

AF:

0.709

Gnomad4 AMR exome

AF:

0.838

Gnomad4 ASJ exome

AF:

0.710

Gnomad4 EAS exome

AF:

0.450

Gnomad4 SAS exome

AF:

0.684

Gnomad4 FIN exome

AF:

0.794

Gnomad4 NFE exome

AF:

0.822

Gnomad4 OTH exome

AF:

0.765

GnomAD4 genome

AF:

0.767

AC:

116723

AN:

152174

Hom.:

45299

Cov.:

AF XY:

0.763

AC XY:

56749

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.713

Gnomad4 AMR

AF:

0.808

Gnomad4 ASJ

AF:

0.714

Gnomad4 EAS

AF:

0.445

Gnomad4 SAS

AF:

0.671

Gnomad4 FIN

AF:

0.790

Gnomad4 NFE

AF:

0.820

Gnomad4 OTH

AF:

0.757

Alfa

AF:

0.762

Hom.:

2360

Bravo

AF:

0.768

Asia WGS

AF:

0.552

AC:

1922

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.7

DANN

Benign

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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