Genetic Variant NM_001370475.1:c.268G>T (chr18-63712604-G-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001370475.1(SERPINB11):c.268G>T(p.Glu90*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 1,613,366 control chromosomes in the GnomAD database, including 386,126 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. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.63 ( 30894 hom., cov: 32)

Exomes 𝑓: 0.69 ( 355232 hom. )

Consequence

SERPINB11
NM_001370475.1 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.11

Publications

40 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINB11	NM_001370475.1 link	c.268G>T	p.Glu90*	stop_gained	Exon 4 of 8	ENST00000544088.6	NP_001357404.1
SERPINB11	NM_080475.5 link	c.268G>T	p.Glu90*	stop_gained	Exon 5 of 9		NP_536723.2	Q96P15F5GYW9A9UKE9
SERPINB11	NM_001291278.2 link	c.268G>T	p.Glu90*	stop_gained	Exon 4 of 6		NP_001278207.1	Q96P15A0A096LPD5A9UKE9
SERPINB11	NM_001291279.2 link	c.-140G>T		5_prime_UTR_variant	Exon 4 of 7		NP_001278208.1	B4DKT7A9UKE9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB11	ENST00000544088.6 link	c.268G>T	p.Glu90*	stop_gained	Exon 4 of 8	2	NM_001370475.1	ENSP00000441497.1		F5GYW9

Frequencies

GnomAD3 genomes

AF:

0.629

AC:

95513

AN:

151926

Hom.:

30877

Cov.:

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.668

Gnomad AMR

AF:

0.593

Gnomad ASJ

AF:

0.655

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.617

Gnomad FIN

AF:

0.670

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.724

Gnomad OTH

AF:

0.644

GnomAD4 exome

AF:

0.693

AC:

1012369

AN:

1461322

Hom.:

355232

Cov.:

AF XY:

0.692

AC XY:

502707

AN XY:

726940

show subpopulations

African (AFR)

AF:

0.489

AC:

16354

AN:

33452

American (AMR)

AF:

0.513

AC:

22930

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.660

AC:

17239

AN:

26130

East Asian (EAS)

AF:

0.414

AC:

16409

AN:

39682

South Asian (SAS)

AF:

0.619

AC:

53352

AN:

86236

European-Finnish (FIN)

AF:

0.667

AC:

35630

AN:

53398

Middle Eastern (MID)

AF:

0.659

AC:

3802

AN:

5768

European-Non Finnish (NFE)

AF:

0.725

AC:

805900

AN:

1111580

Other (OTH)

AF:

0.675

AC:

40753

AN:

60354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

16787

33574

50362

67149

83936

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19822

39644

59466

79288

99110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.629

AC:

95561

AN:

152044

Hom.:

30894

Cov.:

AF XY:

0.623

AC XY:

46346

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.501

AC:

20761

AN:

41460

American (AMR)

AF:

0.593

AC:

9061

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.655

AC:

2272

AN:

3470

East Asian (EAS)

AF:

0.389

AC:

2002

AN:

5152

South Asian (SAS)

AF:

0.619

AC:

2975

AN:

4808

European-Finnish (FIN)

AF:

0.670

AC:

7082

AN:

10578

Middle Eastern (MID)

AF:

0.697

AC:

205

AN:

294

European-Non Finnish (NFE)

AF:

0.724

AC:

49241

AN:

67972

Other (OTH)

AF:

0.641

AC:

1353

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1752

3503

5255

7006

8758

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

782

1564

2346

3128

3910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.684

Hom.:

79195

Bravo

AF:

0.614

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Pathogenic

(source)

PhyloP100

-2.1

Vest4

0.35, 0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over