chr18-63723415-C-T

Variant names:

• chr18-63723415-C-T
• rs953696
• NM_001370475.1:c.*16C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.82).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB11	NM_001370475.1	MANE Select	c.*16C>T		3_prime_UTR	Exon 8 of 8	NP_001357404.1
	SERPINB11	NM_080475.5		c.*16C>T		3_prime_UTR	Exon 9 of 9	NP_536723.2
	SERPINB11	NM_001291278.2		c.*16C>T		3_prime_UTR	Exon 6 of 6	NP_001278207.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINB11	ENST00000544088.6	TSL:2 MANE Select	c.*16C>T		3_prime_UTR	Exon 8 of 8	ENSP00000441497.1
	SERPINB11	ENST00000382749.9	TSL:1	c.*16C>T		3_prime_UTR	Exon 9 of 9	ENSP00000421854.1
	SERPINB11	ENST00000467649.2	TSL:1	n.1029+314C>T		intron	N/A

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

GnomAD2 exomes AF: 0.726 AC: 162538 AN: 224004 AF XY: 0.724

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 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

African (AFR) AF: 0.572 AC: 18632 AN: 32600

American (AMR) AF: 0.743 AC: 30961 AN: 41690

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 16948 AN: 23814

East Asian (EAS) AF: 0.853 AC: 33575 AN: 39340

South Asian (SAS) AF: 0.688 AC: 55318 AN: 80370

European-Finnish (FIN) AF: 0.751 AC: 39214 AN: 52198

Middle Eastern (MID) AF: 0.683 AC: 3799 AN: 5564

European-Non Finnish (NFE) AF: 0.730 AC: 797113 AN: 1091330

Other (OTH) AF: 0.716 AC: 42123 AN: 58838

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

African (AFR) AF: 0.577 AC: 23902 AN: 41410

American (AMR) AF: 0.713 AC: 10890 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2483 AN: 3470

East Asian (EAS) AF: 0.844 AC: 4364 AN: 5168

South Asian (SAS) AF: 0.689 AC: 3316 AN: 4814

European-Finnish (FIN) AF: 0.753 AC: 7948 AN: 10556

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

European-Non Finnish (NFE) AF: 0.726 AC: 49337 AN: 68000

Other (OTH) AF: 0.683 AC: 1432 AN: 2098

Alfa AF: 0.709 Hom.: 51093

Bravo AF: 0.684

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		-0.16
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: rs953696; hg19: chr18-61390649; COSMIC: COSV66956871; COSMIC: COSV66956871;