18-63723599-T-C

Variant names:

• chr18-63723599-T-C
• rs953694
• NM_001370475.1:c.*200T>C

Variant summary

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

The NM_001370475.1(SERPINB11):​c.*200T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 501,904 control chromosomes in the GnomAD database, including 128,223 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 (36513 hom., cov: 32)
  • Exomes 𝑓: 0.72 (91710 hom.)
• Consequence: SERPINB11 NM_001370475.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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=-0.87).
• 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 rank	MANE	Protein	UniProt
SERPINB11	NM_001370475.1	c.*200T>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000544088.6	NP_001357404.1
SERPINB11	NM_080475.5	c.*200T>C		3_prime_UTR_variant	Exon 9 of 9		NP_536723.2
SERPINB11	NM_001291278.2	c.*200T>C		3_prime_UTR_variant	Exon 6 of 6		NP_001278207.1
SERPINB11	NM_001291279.2	c.*200T>C		3_prime_UTR_variant	Exon 7 of 7		NP_001278208.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB11	ENST00000544088.6	c.*200T>C		3_prime_UTR_variant	Exon 8 of 8	2	NM_001370475.1	ENSP00000441497.1

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104721 AN: 152002 Hom.: 36496 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.845

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

GnomAD4 exome AF: 0.721 AC: 252255 AN: 349784 Hom.: 91710 Cov.: 4 AF XY: 0.721 AC XY: 128851 AN XY: 178670

Gnomad4 AFR exome AF: 0.569

Gnomad4 AMR exome AF: 0.726

Gnomad4 ASJ exome AF: 0.711

Gnomad4 EAS exome AF: 0.855

Gnomad4 SAS exome AF: 0.678

Gnomad4 FIN exome AF: 0.747

Gnomad4 NFE exome AF: 0.714

Gnomad4 OTH exome AF: 0.705

GnomAD4 genome AF: 0.689 AC: 104783 AN: 152120 Hom.: 36513 Cov.: 32 AF XY: 0.692 AC XY: 51440 AN XY: 74368

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.682

Alfa AF: 0.700 Hom.: 4723

Bravo AF: 0.684

Asia WGS AF: 0.761 AC: 2645 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
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: rs953694; hg19: chr18-61390833;