18-63493054-T-G

Position:

• chr18-63493054-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002639.5(SERPINB5):​c.526T>G​(p.Ser176Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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. S176P) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SERPINB5 NM_002639.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.00

Genes affected

SERPINB5 (HGNC:8949): (serpin family B member 5) Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity. Predicted to act upstream of or within several processes, including extracellular matrix organization; prostate gland morphogenesis; and regulation of epithelial cell proliferation. Located in cytoplasm. Biomarker of hepatocellular carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1965523).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINB5	NM_002639.5	c.526T>G	p.Ser176Ala	missense_variant	5/7	ENST00000382771.9	NP_002630.2
SERPINB5	XM_006722483.4	c.13T>G	p.Ser5Ala	missense_variant	2/4		XP_006722546.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINB5	ENST00000382771.9	c.526T>G	p.Ser176Ala	missense_variant	5/7	1	NM_002639.5	ENSP00000372221.4
SERPINB5	ENST00000489441.5	c.526T>G	p.Ser176Ala	missense_variant	5/5	1		ENSP00000467158.1
SERPINB5	ENST00000464346.1	n.208T>G		non_coding_transcript_exon_variant	2/4	3
SERPINB5	ENST00000465652.5	n.199T>G		non_coding_transcript_exon_variant	2/4	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 61

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.076	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	21
DANN	Benign	0.96
DEOGEN2	Benign	0.28	T;.
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.12
FATHMM_MKL	Benign	0.64	D
LIST_S2	Benign	0.26	T;T
M_CAP	Uncertain	0.089	D
MetaRNN	Benign	0.20	T;T
MetaSVM	Benign	-0.45	T
MutationAssessor	Benign	0.83	L;L
PrimateAI	Benign	0.45	T
PROVEAN	Benign	-0.75	N;.
REVEL	Benign	0.21
Sift	Benign	0.45	T;.
Sift4G	Benign	0.71	T;T
Polyphen		0.0	B;B
Vest4		0.079
MutPred		0.30		Loss of phosphorylation at S176 (P = 0.0597);Loss of phosphorylation at S176 (P = 0.0597);
MVP		0.76
MPC		0.052
ClinPred		0.16	T
GERP RS		6.0
Varity_R		0.18
gMVP		0.72

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

LitVar

Other links and lift over

dbSNP: rs2289519; hg19: chr18-61160287;