2-223980202-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001136528.2(SERPINE2):c.1072+109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 735,092 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
SERPINE2
NM_001136528.2 intron
NM_001136528.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.252
Publications
11 publications found
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 was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS2
High AC in GnomAdExome4 at 15 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SERPINE2 | NM_001136528.2 | c.1072+109G>A | intron_variant | Intron 7 of 8 | ENST00000409304.6 | NP_001130000.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SERPINE2 | ENST00000409304.6 | c.1072+109G>A | intron_variant | Intron 7 of 8 | 1 | NM_001136528.2 | ENSP00000386412.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.0000204 AC: 15AN: 735092Hom.: 0 Cov.: 10 AF XY: 0.0000285 AC XY: 11AN XY: 385756 show subpopulations
GnomAD4 exome
AF:
AC:
15
AN:
735092
Hom.:
Cov.:
10
AF XY:
AC XY:
11
AN XY:
385756
show subpopulations
African (AFR)
AF:
AC:
0
AN:
19010
American (AMR)
AF:
AC:
0
AN:
37804
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19164
East Asian (EAS)
AF:
AC:
0
AN:
33742
South Asian (SAS)
AF:
AC:
15
AN:
63824
European-Finnish (FIN)
AF:
AC:
0
AN:
49116
Middle Eastern (MID)
AF:
AC:
0
AN:
3308
European-Non Finnish (NFE)
AF:
AC:
0
AN:
473356
Other (OTH)
AF:
AC:
0
AN:
35768
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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