rs192949139

Variant names:

• chr18-63637811-C-A
• NM_002974.4:c.1081G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-63637811-C-A
• chr18-63637811-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002974.4(SERPINB4):​c.1081G>T​(p.Glu361*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SERPINB4 NM_002974.4 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

Genes affected

SERPINB4 (HGNC:10570): (serpin family B member 4) The protein encoded by this gene is a member of the serpin family of serine protease inhibitors. The encoded protein is highly expressed in many tumor cells and can inactivate granzyme M, an enzyme that kills tumor cells. This protein, along with serpin B3, can be processed into smaller fragments that aggregate to form an autoantigen in psoriasis, probably by causing chronic inflammation. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINB4	NM_002974.4	c.1081G>T	p.Glu361*	stop_gained	Exon 8 of 8	ENST00000341074.10	NP_002965.1
SERPINB4	NM_175041.2	c.1018G>T	p.Glu340*	stop_gained	Exon 8 of 8		NP_778206.1
SERPINB4	XM_011526138.2	c.1081G>T	p.Glu361*	stop_gained	Exon 8 of 8		XP_011524440.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB4	ENST00000341074.10	c.1081G>T	p.Glu361*	stop_gained	Exon 8 of 8	1	NM_002974.4	ENSP00000343445.5
SERPINB4	ENST00000413673.5	c.1021G>T	p.Glu341*	stop_gained	Exon 7 of 7	1		ENSP00000398645.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.33	D
BayesDel_noAF	Pathogenic	0.24
CADD	Pathogenic	34
DANN	Benign	0.95
Eigen	Benign	-0.057
Eigen_PC	Benign	-0.45
FATHMM_MKL	Benign	0.21	N
Vest4		0.069
ClinPred		0.68	D
GERP RS		0.36

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-61305045;