rs9320032

Variant names:

• chr18-63893977-T-C
• rs9320032
• NM_002575.3:c.169-1287T>C

Variant summary

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

The NM_002575.3(SERPINB2):​c.169-1287T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,068 control chromosomes in the GnomAD database, including 2,835 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 0.18 (2835 hom., cov: 32)
• Consequence: SERPINB2 NM_002575.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 6 publications found

Genes affected

SERPINB2 (HGNC:8584): (serpin family B member 2) Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LOC124904356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINB2	NM_002575.3	c.169-1287T>C		intron_variant	Intron 2 of 7	ENST00000299502.9	NP_002566.1
SERPINB2	NM_001143818.2	c.169-1287T>C		intron_variant	Intron 3 of 8		NP_001137290.1
SERPINB2	XM_024451192.2	c.169-1287T>C		intron_variant	Intron 2 of 7		XP_024306960.1
LOC124904356	XR_007066466.1	n.84+476A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB2	ENST00000299502.9	c.169-1287T>C		intron_variant	Intron 2 of 7	1	NM_002575.3	ENSP00000299502.4

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27833 AN: 151950 Hom.: 2830 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.183 AC: 27854 AN: 152068 Hom.: 2835 Cov.: 32 AF XY: 0.186 AC XY: 13803 AN XY: 74324

African (AFR) AF: 0.111 AC: 4617 AN: 41504

American (AMR) AF: 0.293 AC: 4481 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3468

East Asian (EAS) AF: 0.220 AC: 1134 AN: 5150

South Asian (SAS) AF: 0.205 AC: 989 AN: 4814

European-Finnish (FIN) AF: 0.194 AC: 2048 AN: 10570

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13395 AN: 67972

Other (OTH) AF: 0.212 AC: 448 AN: 2114

Alfa AF: 0.198 Hom.: 5326

Bravo AF: 0.188

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.53
PhyloP100		-0.0020
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: rs9320032; hg19: chr18-61561211;