rs6747096
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001136528.2(SERPINE2):āc.477T>Cā(p.Asn159=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,612,994 control chromosomes in the GnomAD database, including 38,675 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: š 0.26 ( 6405 hom., cov: 33)
Exomes š: 0.20 ( 32270 hom. )
Consequence
SERPINE2
NM_001136528.2 synonymous
NM_001136528.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.338
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP7
?
Synonymous conserved (PhyloP=0.338 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINE2 | NM_001136528.2 | c.477T>C | p.Asn159= | synonymous_variant | 3/9 | ENST00000409304.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINE2 | ENST00000409304.6 | c.477T>C | p.Asn159= | synonymous_variant | 3/9 | 1 | NM_001136528.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.263 AC: 39996AN: 152038Hom.: 6391 Cov.: 33
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GnomAD3 exomes AF: 0.197 AC: 49459AN: 251120Hom.: 5792 AF XY: 0.196 AC XY: 26624AN XY: 135716
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GnomAD4 exome AF: 0.203 AC: 295851AN: 1460838Hom.: 32270 Cov.: 32 AF XY: 0.202 AC XY: 146815AN XY: 726750
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GnomAD4 genome ? AF: 0.263 AC: 40043AN: 152156Hom.: 6405 Cov.: 33 AF XY: 0.258 AC XY: 19187AN XY: 74394
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at