Variant chr11-130160143-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000278742.6(ST14):c.81+83C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 993,234 control chromosomes in the GnomAD database, including 1,135 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.049 ( 251 hom., cov: 32)

Exomes 𝑓: 0.041 ( 884 hom. )

Consequence

ST14
ENST00000278742.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.00100

Variant links:

Genes affected

ST14 (HGNC:11344): (ST14 transmembrane serine protease matriptase) The protein encoded by this gene is an epithelial-derived, integral membrane serine protease. This protease forms a complex with the Kunitz-type serine protease inhibitor, HAI-1, and is found to be activated by sphingosine 1-phosphate. This protease has been shown to cleave and activate hepatocyte growth factor/scattering factor, and urokinase plasminogen activator, which suggest the function of this protease as an epithelial membrane activator for other proteases and latent growth factors. The expression of this protease has been associated with breast, colon, prostate, and ovarian tumors, which implicates its role in cancer invasion, and metastasis. [provided by RefSeq, Jul 2008]

ST14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 11-130160143-C-T is Benign according to our data. Variant chr11-130160143-C-T is described in ClinVar as [Benign]. Clinvar id is 1287856.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST14	NM_021978.4 linkuse as main transcript	c.81+83C>T		intron_variant		ENST00000278742.6	NP_068813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST14	ENST00000278742.6 linkuse as main transcript	c.81+83C>T		intron_variant		1	NM_021978.4	ENSP00000278742	P1

Frequencies

GnomAD3 genomes

AF:

0.0488

AC:

7422

AN:

152038

Hom.:

252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0678

Gnomad AMI

AF:

0.0549

Gnomad AMR

AF:

0.0323

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.0410

Gnomad FIN

AF:

0.0327

Gnomad MID

AF:

0.0385

Gnomad NFE

AF:

0.0375

Gnomad OTH

AF:

0.0436

GnomAD4 exome

AF:

0.0409

AC:

34385

AN:

841086

Hom.:

884

AF XY:

0.0405

AC XY:

16656

AN XY:

410864

show subpopulations

Gnomad4 AFR exome

AF:

0.0729

Gnomad4 AMR exome

AF:

0.0291

Gnomad4 ASJ exome

AF:

0.0296

Gnomad4 EAS exome

AF:

0.131

Gnomad4 SAS exome

AF:

0.0426

Gnomad4 FIN exome

AF:

0.0326

Gnomad4 NFE exome

AF:

0.0374

Gnomad4 OTH exome

AF:

0.0449

GnomAD4 genome

AF:

0.0488

AC:

7426

AN:

152148

Hom.:

251

Cov.:

AF XY:

0.0489

AC XY:

3634

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.0679

Gnomad4 AMR

AF:

0.0321

Gnomad4 ASJ

AF:

0.0274

Gnomad4 EAS

AF:

0.151

Gnomad4 SAS

AF:

0.0404

Gnomad4 FIN

AF:

0.0327

Gnomad4 NFE

AF:

0.0375

Gnomad4 OTH

AF:

0.0441

Alfa

AF:

0.0401

Hom.:

136

Bravo

AF:

0.0510

Asia WGS

AF:

0.0860

AC:

298

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

7.5

DANN

Benign

0.94

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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