NM_001136528.2:c.-23+7378T>C

Variant names:

• chr2-224031721-A-G
• rs1020118
• NM_001136528.2:c.-23+7378T>C

Variant summary

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

The NM_001136528.2(SERPINE2):​c.-23+7378T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 149,612 control chromosomes in the GnomAD database, including 31,874 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 0.65 (31874 hom., cov: 26)
• Consequence: SERPINE2 NM_001136528.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• 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=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINE2	NM_001136528.2	c.-23+7378T>C		intron_variant	Intron 1 of 8	ENST00000409304.6	NP_001130000.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINE2	ENST00000409304.6	c.-23+7378T>C		intron_variant	Intron 1 of 8	1	NM_001136528.2	ENSP00000386412.1

Frequencies

GnomAD3 genomes AF: 0.651 AC: 97276 AN: 149488 Hom.: 31851 Cov.: 26

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.651 AC: 97351 AN: 149612 Hom.: 31874 Cov.: 26 AF XY: 0.656 AC XY: 47765 AN XY: 72856

African (AFR) AF: 0.612 AC: 24709 AN: 40378

American (AMR) AF: 0.702 AC: 10507 AN: 14974

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2289 AN: 3462

East Asian (EAS) AF: 0.590 AC: 2935 AN: 4972

South Asian (SAS) AF: 0.710 AC: 3372 AN: 4746

European-Finnish (FIN) AF: 0.721 AC: 7205 AN: 9992

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.652 AC: 44232 AN: 67804

Other (OTH) AF: 0.636 AC: 1327 AN: 2088

Alfa AF: 0.651 Hom.: 8738

Bravo AF: 0.649

Asia WGS AF: 0.629 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.53
PhyloP100		1.3
PromoterAI		0.0040	Neutral
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: rs1020118; hg19: chr2-224896438;