ENST00000489748.5:c.-15-8271C>G

Variant names:

• chr18-63701908-C-G
• rs8083794
• ENST00000489748.5:c.-15-8271C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB11	ENST00000489748.5	c.-15-8271C>G		intron_variant	Intron 2 of 6	2		ENSP00000480275.1

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

African (AFR) AF: 0.499 AC: 20685 AN: 41444

American (AMR) AF: 0.407 AC: 6225 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2742 AN: 5162

South Asian (SAS) AF: 0.378 AC: 1823 AN: 4820

European-Finnish (FIN) AF: 0.330 AC: 3485 AN: 10576

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18737 AN: 67968

Other (OTH) AF: 0.359 AC: 757 AN: 2108

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
PhyloP100		-0.021
PromoterAI		-0.0024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8083794; hg19: chr18-61369142;