18-63701591-C-G

Variant names:

• chr18-63701591-C-G
• rs1403299
• ENST00000489748.5:c.-15-8588C>G

Variant summary

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

The ENST00000489748.5(SERPINB11):​c.-15-8588C>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 151,920 control chromosomes in the GnomAD database, including 11,117 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 (11117 hom., cov: 31)
• Consequence: SERPINB11 ENST00000489748.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 3 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=-0.88).
• 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.-15-8588C>G		intron_variant	Intron 2 of 6	2		ENSP00000480275.1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55954 AN: 151802 Hom.: 11088 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.369 AC: 56026 AN: 151920 Hom.: 11117 Cov.: 31 AF XY: 0.373 AC XY: 27717 AN XY: 74220

African (AFR) AF: 0.500 AC: 20698 AN: 41430

American (AMR) AF: 0.406 AC: 6202 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1191 AN: 3460

East Asian (EAS) AF: 0.532 AC: 2741 AN: 5156

South Asian (SAS) AF: 0.378 AC: 1817 AN: 4802

European-Finnish (FIN) AF: 0.330 AC: 3478 AN: 10542

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

European-Non Finnish (NFE) AF: 0.276 AC: 18747 AN: 67956

Other (OTH) AF: 0.360 AC: 760 AN: 2112

Alfa AF: 0.165 Hom.: 303

Bravo AF: 0.382

Asia WGS AF: 0.488 AC: 1695 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1403299; hg19: chr18-61368825;