18-63723415-C-T

Position:

• chr18-63723415-C-T

Variant summary

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

The NM_001370475.1(SERPINB11):​c.*16C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 1,577,738 control chromosomes in the GnomAD database, including 415,306 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 0.69 (36466 hom., cov: 31)
  • Exomes 𝑓: 0.73 (378840 hom.)
• Consequence: SERPINB11 NM_001370475.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINB11	NM_001370475.1	c.*16C>T		3_prime_UTR_variant	8/8	ENST00000544088.6	NP_001357404.1
SERPINB11	NM_001291278.2	c.*16C>T		3_prime_UTR_variant	6/6		NP_001278207.1
SERPINB11	NM_001291279.2	c.*16C>T		3_prime_UTR_variant	7/7		NP_001278208.1
SERPINB11	NM_080475.5	c.*16C>T		3_prime_UTR_variant	9/9		NP_536723.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINB11	ENST00000544088.6	c.*16C>T		3_prime_UTR_variant	8/8	2	NM_001370475.1	ENSP00000441497	P1

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104624 AN: 151876 Hom.: 36449 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.686

GnomAD3 exomes AF: 0.726 AC: 162538 AN: 224004 Hom.: 59189 AF XY: 0.724 AC XY: 87417 AN XY: 120686

Gnomad AFR exome AF: 0.580

Gnomad AMR exome AF: 0.749

Gnomad ASJ exome AF: 0.712

Gnomad EAS exome AF: 0.845

Gnomad SAS exome AF: 0.686

Gnomad FIN exome AF: 0.754

Gnomad NFE exome AF: 0.724

Gnomad OTH exome AF: 0.725

GnomAD4 exome AF: 0.728 AC: 1037683 AN: 1425744 Hom.: 378840 Cov.: 37 AF XY: 0.727 AC XY: 512154 AN XY: 704870

Gnomad4 AFR exome AF: 0.572

Gnomad4 AMR exome AF: 0.743

Gnomad4 ASJ exome AF: 0.712

Gnomad4 EAS exome AF: 0.853

Gnomad4 SAS exome AF: 0.688

Gnomad4 FIN exome AF: 0.751

Gnomad4 NFE exome AF: 0.730

Gnomad4 OTH exome AF: 0.716

GnomAD4 genome AF: 0.689 AC: 104686 AN: 151994 Hom.: 36466 Cov.: 31 AF XY: 0.692 AC XY: 51389 AN XY: 74280

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.683

Alfa AF: 0.715 Hom.: 40135

Bravo AF: 0.684

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs953696; hg19: chr18-61390649; COSMIC: COSV66956871; COSMIC: COSV66956871;