2-224001799-CGT-ACG

Variant names:

• chr2-224001799-CGT-ACG
• NM_001136528.2:c.100_102delACGinsCGT
• SERPINE2 p.Thr34Arg

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001136528.2(SERPINE2):​c.100_102delACGinsCGT​(p.Thr34Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T34M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SERPINE2 NM_001136528.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 0 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINE2	NM_001136528.2	MANE Select	c.100_102delACGinsCGT	p.Thr34Arg	missense	N/A	NP_001130000.1	P07093-2
	SERPINE2	NM_001136530.1		c.136_138delACGinsCGT	p.Thr46Arg	missense	N/A	NP_001130002.1	P07093-3
	SERPINE2	NM_006216.4		c.100_102delACGinsCGT	p.Thr34Arg	missense	N/A	NP_006207.1	P07093-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINE2	ENST00000409304.6	TSL:1 MANE Select	c.100_102delACGinsCGT	p.Thr34Arg	missense	N/A	ENSP00000386412.1	P07093-2
	SERPINE2	ENST00000258405.9	TSL:1	c.100_102delACGinsCGT	p.Thr34Arg	missense	N/A	ENSP00000258405.4	P07093-1
	SERPINE2	ENST00000409840.7	TSL:1	c.100_102delACGinsCGT	p.Thr34Arg	missense	N/A	ENSP00000386969.3	P07093-2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr2-224866516;