rs1530021

Variant summary

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

The NM_001136528.2(SERPINE2):​c.-22-4597T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,968 control chromosomes in the GnomAD database, including 35,742 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 0.68 ( 35742 hom., cov: 31)

Consequence

SERPINE2
NM_001136528.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232
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]

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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 = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SERPINE2NM_001136528.2 linkuse as main transcriptc.-22-4597T>C intron_variant ENST00000409304.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SERPINE2ENST00000409304.6 linkuse as main transcriptc.-22-4597T>C intron_variant 1 NM_001136528.2 A1P07093-2

Frequencies

GnomAD3 genomes
AF:
0.681
AC:
103476
AN:
151850
Hom.:
35751
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.560
Gnomad AMI
AF:
0.576
Gnomad AMR
AF:
0.703
Gnomad ASJ
AF:
0.711
Gnomad EAS
AF:
0.574
Gnomad SAS
AF:
0.737
Gnomad FIN
AF:
0.736
Gnomad MID
AF:
0.668
Gnomad NFE
AF:
0.745
Gnomad OTH
AF:
0.698
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.681
AC:
103505
AN:
151968
Hom.:
35742
Cov.:
31
AF XY:
0.683
AC XY:
50732
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.560
Gnomad4 AMR
AF:
0.703
Gnomad4 ASJ
AF:
0.711
Gnomad4 EAS
AF:
0.573
Gnomad4 SAS
AF:
0.735
Gnomad4 FIN
AF:
0.736
Gnomad4 NFE
AF:
0.745
Gnomad4 OTH
AF:
0.692
Alfa
AF:
0.692
Hom.:
4566
Bravo
AF:
0.671
Asia WGS
AF:
0.613
AC:
2131
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
2.4
DANN
Benign
0.35

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.

Other links and lift over

dbSNP: rs1530021; hg19: chr2-224871236; API