Variant 18-63589679-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_012397.4(SERPINB13):c.189G>A(p.Thr63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00716 in 1,613,532 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0048 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0074 ( 50 hom. )

Consequence

SERPINB13
NM_012397.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.587

Variant links:

Genes affected

SERPINB13 (HGNC:8944): (serpin family B member 13) The protein encoded by this gene is a member of the serpin family of serine protease inhibitors. The encoded protein inhibits the activity of cathepsin K and is itself transcriptionally repressed by RUNX1. This gene is downregulated in many types of cancer. [provided by RefSeq, Jan 2017]

SERPINB13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 18-63589679-G-A is Benign according to our data. Variant chr18-63589679-G-A is described in ClinVar as [Benign]. Clinvar id is 788137.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.587 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERPINB13	NM_012397.4 linkuse as main transcript	c.189G>A	p.Thr63=	synonymous_variant	3/8	ENST00000344731.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPINB13	ENST00000344731.10 linkuse as main transcript	c.189G>A	p.Thr63=	synonymous_variant	3/8	1	NM_012397.4	P1	Q9UIV8-1

Frequencies

GnomAD3 genomes

AF:

0.00484

AC:

735

AN:

151996

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00420

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00601

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00819

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00596

AC:

1495

AN:

250980

Hom.:

AF XY:

0.00621

AC XY:

842

AN XY:

135628

show subpopulations

Gnomad AFR exome

AF:

0.00142

Gnomad AMR exome

AF:

0.00359

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00588

Gnomad FIN exome

AF:

0.00370

Gnomad NFE exome

AF:

0.00922

Gnomad OTH exome

AF:

0.00653

GnomAD4 exome

AF:

0.00741

AC:

10825

AN:

1461418

Hom.:

Cov.:

AF XY:

0.00736

AC XY:

5349

AN XY:

726994

show subpopulations

Gnomad4 AFR exome

AF:

0.00152

Gnomad4 AMR exome

AF:

0.00344

Gnomad4 ASJ exome

AF:

0.000344

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00594

Gnomad4 FIN exome

AF:

0.00393

Gnomad4 NFE exome

AF:

0.00855

Gnomad4 OTH exome

AF:

0.00619

GnomAD4 genome

AF:

0.00483

AC:

735

AN:

152114

Hom.:

Cov.:

AF XY:

0.00464

AC XY:

345

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00419

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.00198

Gnomad4 NFE

AF:

0.00819

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00660

Hom.:

Bravo

AF:

0.00501

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.00720

EpiControl

AF:

0.00741

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.2

DANN

Benign

0.33

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over