Variant rs1506418 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001370475.1(SERPINB11):c.541G>A(p.Ala181Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,600,626 control chromosomes in the GnomAD database, including 83,935 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 ( 11310 hom., cov: 33)

Exomes 𝑓: 0.31 ( 72625 hom. )

Consequence

SERPINB11
NM_001370475.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.60

Variant links:

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]

SERPINB11 links:

SERPINB11 (HGNC:):

SERPINB11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.375875E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINB11	NM_001370475.1 linkuse as main transcript	c.541G>A	p.Ala181Thr	missense_variant	6/8	ENST00000544088.6	NP_001357404.1
SERPINB11	NM_080475.5 linkuse as main transcript	c.541G>A	p.Ala181Thr	missense_variant	7/9		NP_536723.2	Q96P15F5GYW9A9UKE9
SERPINB11	NM_001291279.2 linkuse as main transcript	c.16G>A	p.Ala6Thr	missense_variant	5/7		NP_001278208.1	B4DKT7A9UKE9
SERPINB11	NM_001291278.2 linkuse as main transcript	c.358-753G>A		intron_variant			NP_001278207.1	Q96P15A0A096LPD5A9UKE9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINB11	ENST00000544088.6 linkuse as main transcript	c.541G>A	p.Ala181Thr	missense_variant	6/8	2	NM_001370475.1	ENSP00000441497.1		F5GYW9

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56339

AN:

151794

Hom.:

11282

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.275

Gnomad OTH

AF:

0.355

GnomAD3 exomes

AF:

0.364

AC:

89590

AN:

246142

Hom.:

18088

AF XY:

0.354

AC XY:

47293

AN XY:

133606

show subpopulations

Gnomad AFR exome

AF:

0.502

Gnomad AMR exome

AF:

0.496

Gnomad ASJ exome

AF:

0.331

Gnomad EAS exome

AF:

0.606

Gnomad SAS exome

AF:

0.378

Gnomad FIN exome

AF:

0.335

Gnomad NFE exome

AF:

0.273

Gnomad OTH exome

AF:

0.332

GnomAD4 exome

AF:

0.305

AC:

441919

AN:

1448714

Hom.:

72625

Cov.:

AF XY:

0.306

AC XY:

220970

AN XY:

721040

show subpopulations

Gnomad4 AFR exome

AF:

0.509

Gnomad4 AMR exome

AF:

0.486

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.586

Gnomad4 SAS exome

AF:

0.380

Gnomad4 FIN exome

AF:

0.332

Gnomad4 NFE exome

AF:

0.273

Gnomad4 OTH exome

AF:

0.323

GnomAD4 genome

AF:

0.371

AC:

56409

AN:

151912

Hom.:

11310

Cov.:

AF XY:

0.376

AC XY:

27950

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.499

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.345

Gnomad4 EAS

AF:

0.608

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.331

Gnomad4 NFE

AF:

0.276

Gnomad4 OTH

AF:

0.359

Alfa

AF:

0.305

Hom.:

17878

Bravo

AF:

0.386

TwinsUK

AF:

0.273

AC:

1012

ALSPAC

AF:

0.269

AC:

1037

ESP6500AA

AF:

0.495

AC:

1799

ESP6500EA

AF:

0.272

AC:

2217

ExAC

AF:

0.361

AC:

43581

Asia WGS

AF:

0.508

AC:

1763

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Uncertain

0.020

CADD

Uncertain

DANN

Uncertain

1.0

Eigen

Uncertain

0.40

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.83

T;.;T

MetaRNN

Benign

0.00044

T;T;T

MetaSVM

Benign

-0.95

PrimateAI

Uncertain

0.55

PROVEAN

Uncertain

-3.1

.;.;D

REVEL

Uncertain

0.48

Sift4G

Pathogenic

0.0

D;D;D

Polyphen

0.99

.;D;D

Vest4

0.25, 0.25

MPC

0.081

ClinPred

0.022

GERP RS

5.5

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over