Variant rs33916072 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+164T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 553,892 control chromosomes in the GnomAD database, including 54,708 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 0.38 ( 12545 hom., cov: 33)

Exomes 𝑓: 0.45 ( 42163 hom. )

Consequence

SERPINE2
NM_001136528.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.242

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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINE2	NM_001136528.2 link	c.1072+164T>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+164T>C		intron_variant		1	NM_001136528.2	ENSP00000386412.1		P07093-2

Frequencies

GnomAD3 genomes

AF:

0.381

AC:

57892

AN:

152054

Hom.:

12548

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.401

Gnomad AMR

AF:

0.398

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.561

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.483

Gnomad OTH

AF:

0.381

GnomAD4 exome

AF:

0.447

AC:

179640

AN:

401720

Hom.:

42163

Cov.:

AF XY:

0.448

AC XY:

94481

AN XY:

210984

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.406

Gnomad4 ASJ exome

AF:

0.328

Gnomad4 EAS exome

AF:

0.242

Gnomad4 SAS exome

AF:

0.471

Gnomad4 FIN exome

AF:

0.548

Gnomad4 NFE exome

AF:

0.478

Gnomad4 OTH exome

AF:

0.421

GnomAD4 genome

AF:

0.381

AC:

57904

AN:

152172

Hom.:

12545

Cov.:

AF XY:

0.384

AC XY:

28554

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.171

Gnomad4 AMR

AF:

0.398

Gnomad4 ASJ

AF:

0.324

Gnomad4 EAS

AF:

0.247

Gnomad4 SAS

AF:

0.474

Gnomad4 FIN

AF:

0.561

Gnomad4 NFE

AF:

0.483

Gnomad4 OTH

AF:

0.376

Alfa

AF:

0.424

Hom.:

1807

Bravo

AF:

0.355

Asia WGS

AF:

0.340

AC:

1183

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.47

DANN

Benign

0.82

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