chr2-224008973-G-A

Variant names:

• chr2-224008973-G-A
• rs7590948
• NM_001136528.2:c.-22-7051C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136528.2(SERPINE2):​c.-22-7051C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,848 control chromosomes in the GnomAD database, including 16,235 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 0.43 (16235 hom., cov: 31)
• Consequence: SERPINE2 NM_001136528.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• Publications: 9 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]

ENSG00000310283 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136528.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINE2	NM_001136528.2	MANE Select	c.-22-7051C>T		intron	N/A	NP_001130000.1
	SERPINE2	NM_001136530.1		c.15-7051C>T		intron	N/A	NP_001130002.1
	SERPINE2	NM_006216.4		c.-22-7051C>T		intron	N/A	NP_006207.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINE2	ENST00000409304.6	TSL:1 MANE Select	c.-22-7051C>T		intron	N/A	ENSP00000386412.1
	SERPINE2	ENST00000258405.9	TSL:1	c.-22-7051C>T		intron	N/A	ENSP00000258405.4
	SERPINE2	ENST00000409840.7	TSL:1	c.-22-7051C>T		intron	N/A	ENSP00000386969.3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64740 AN: 151730 Hom.: 16246 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.445

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.426 AC: 64733 AN: 151848 Hom.: 16235 Cov.: 31 AF XY: 0.433 AC XY: 32088 AN XY: 74158

African (AFR) AF: 0.147 AC: 6105 AN: 41492

American (AMR) AF: 0.498 AC: 7607 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2002 AN: 5144

South Asian (SAS) AF: 0.568 AC: 2735 AN: 4812

European-Finnish (FIN) AF: 0.609 AC: 6390 AN: 10486

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37016 AN: 67872

Other (OTH) AF: 0.441 AC: 928 AN: 2104

Alfa AF: 0.501 Hom.: 27593

Bravo AF: 0.402

Asia WGS AF: 0.468 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.56
PhyloP100		0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7590948; hg19: chr2-224873690;