rs8083794

chr18-63701908-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000489748.5(SERPINB11):c.-15-8271C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,042 control chromosomes in the GnomAD database, including 11,116 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 0.37 (11116 hom., cov: 32)
• Consequence: SERPINB11 ENST00000489748.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

SERPINB11 (HGNC:14221): (serpin family B member 11) Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity. Predicted to be located in cytoplasm. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPINB11	ENST00000489748.5	c.-15-8271C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55969 AN: 151924 Hom.: 11087 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.369 AC: 56041 AN: 152042 Hom.: 11116 Cov.: 32 AF XY: 0.373 AC XY: 27727 AN XY: 74330

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.359

Alfa AF: 0.323 Hom.: 1058

Bravo AF: 0.382

Asia WGS AF: 0.488 AC: 1697 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	3.0
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8083794; hg19: chr18-61369142;