rs1509476

Variant names:

• chr18-63495126-G-A
• rs1509476
• NM_002639.5:c.567+2031G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-63495126-G-A
• chr18-63495126-G-C
• chr18-63495126-G-T

Variant summary

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

The NM_002639.5(SERPINB5):​c.567+2031G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,150 control chromosomes in the GnomAD database, including 41,986 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 0.74 (41986 hom., cov: 32)
• Consequence: SERPINB5 NM_002639.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINB5	NM_002639.5	c.567+2031G>A		intron_variant	Intron 5 of 6	ENST00000382771.9	NP_002630.2
SERPINB5	XM_006722483.4	c.54+2031G>A		intron_variant	Intron 2 of 3		XP_006722546.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB5	ENST00000382771.9	c.567+2031G>A		intron_variant	Intron 5 of 6	1	NM_002639.5	ENSP00000372221.4
SERPINB5	ENST00000464346.1	n.249+2031G>A		intron_variant	Intron 2 of 3	3
SERPINB5	ENST00000465652.5	n.240+2031G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112409 AN: 152032 Hom.: 41943 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.739 AC: 112506 AN: 152150 Hom.: 41986 Cov.: 32 AF XY: 0.735 AC XY: 54655 AN XY: 74386

African (AFR) AF: 0.846 AC: 35128 AN: 41522

American (AMR) AF: 0.709 AC: 10837 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2367 AN: 3468

East Asian (EAS) AF: 0.779 AC: 4033 AN: 5174

South Asian (SAS) AF: 0.692 AC: 3343 AN: 4828

European-Finnish (FIN) AF: 0.655 AC: 6930 AN: 10578

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47428 AN: 67974

Other (OTH) AF: 0.731 AC: 1542 AN: 2110

Alfa AF: 0.718 Hom.: 4871

Bravo AF: 0.745

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.44
PhyloP100		-0.56
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: rs1509476; hg19: chr18-61162359;