18-63723599-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370475.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB11	NM_001370475.1	MANE Select	c.*200T>C		3_prime_UTR	Exon 8 of 8	NP_001357404.1	F5GYW9
	SERPINB11	NM_080475.5		c.*200T>C		3_prime_UTR	Exon 9 of 9	NP_536723.2	Q96P15-1
	SERPINB11	NM_001291278.2		c.*200T>C		3_prime_UTR	Exon 6 of 6	NP_001278207.1	A0A096LPD5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB11	ENST00000544088.6	TSL:2 MANE Select	c.*200T>C		3_prime_UTR	Exon 8 of 8	ENSP00000441497.1	F5GYW9
	SERPINB11	ENST00000382749.9	TSL:1	c.*200T>C		3_prime_UTR	Exon 9 of 9	ENSP00000421854.1	Q96P15-1
	SERPINB11	ENST00000467649.2	TSL:1	n.1029+498T>C		intron	N/A

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

African (AFR) AF: 0.569 AC: 5997 AN: 10534

American (AMR) AF: 0.726 AC: 9001 AN: 12404

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 8188 AN: 11514

East Asian (EAS) AF: 0.855 AC: 23419 AN: 27376

South Asian (SAS) AF: 0.678 AC: 11351 AN: 16734

European-Finnish (FIN) AF: 0.747 AC: 19396 AN: 25954

Middle Eastern (MID) AF: 0.678 AC: 1117 AN: 1648

European-Non Finnish (NFE) AF: 0.714 AC: 158562 AN: 222032

Other (OTH) AF: 0.705 AC: 15224 AN: 21588

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

African (AFR) AF: 0.577 AC: 23946 AN: 41486

American (AMR) AF: 0.713 AC: 10896 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2483 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4377 AN: 5180

South Asian (SAS) AF: 0.689 AC: 3322 AN: 4824

European-Finnish (FIN) AF: 0.753 AC: 7974 AN: 10584

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49330 AN: 67978

Other (OTH) AF: 0.682 AC: 1441 AN: 2112

Alfa AF: 0.706 Hom.: 11024

Bravo AF: 0.684

Asia WGS AF: 0.761 AC: 2645 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs953694; hg19: chr18-61390833;