Genetic Variant NM_001370475.1:c.*200T>C (chr18-63723599-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.121

Publications

4 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SERPINB11	NM_001370475.1 link	c.*200T>C	3_prime_UTR_variant	Exon 8 of 8	ENST00000544088.6	NP_001357404.1
SERPINB11	NM_080475.5 link	c.*200T>C	3_prime_UTR_variant	Exon 9 of 9		NP_536723.2	Q96P15F5GYW9A9UKE9
SERPINB11	NM_001291278.2 link	c.*200T>C	3_prime_UTR_variant	Exon 6 of 6		NP_001278207.1	Q96P15A0A096LPD5A9UKE9
SERPINB11	NM_001291279.2 link	c.*200T>C	3_prime_UTR_variant	Exon 7 of 7		NP_001278208.1	B4DKT7A9UKE9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB11	ENST00000544088.6 link	c.*200T>C		3_prime_UTR_variant	Exon 8 of 8	2	NM_001370475.1	ENSP00000441497.1		F5GYW9

Frequencies

GnomAD3 genomes

AF:

0.689

AC:

104721

AN:

152002

Hom.:

36496

Cov.:

show subpopulations

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.:

AF XY:

0.721

AC XY:

128851

AN XY:

178670

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

3146

6292

9437

12583

15729

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

924

1848

2772

3696

4620

<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:

0.689

AC:

104783

AN:

152120

Hom.:

36513

Cov.:

AF XY:

0.692

AC XY:

51440

AN XY:

74368

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1661

3322

4983

6644

8305

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.706

Hom.:

11024

Bravo

AF:

0.684

Asia WGS

AF:

0.761

AC:

2645

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.4

(source)

DANN

Benign

0.52

PhyloP100

0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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