Variant 11-130188152-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_021978.4(ST14):c.120A>G(p.Pro40=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 1,614,114 control chromosomes in the GnomAD database, including 4,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1863 hom., cov: 33)

Exomes 𝑓: 0.046 ( 2803 hom. )

Consequence

ST14
NM_021978.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.81

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 11-130188152-A-G is Benign according to our data. Variant chr11-130188152-A-G is described in ClinVar as [Benign]. Clinvar id is 1599867.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.81 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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.120A>G	p.Pro40=	synonymous_variant	2/19	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.120A>G	p.Pro40=	synonymous_variant	2/19	1	NM_021978.4	ENSP00000278742	P1

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16425

AN:

152126

Hom.:

1851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0649

Gnomad ASJ

AF:

0.0905

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.00932

Gnomad FIN

AF:

0.0259

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0419

Gnomad OTH

AF:

0.0995

GnomAD3 exomes

AF:

0.0514

AC:

12912

AN:

251162

Hom.:

887

AF XY:

0.0458

AC XY:

6221

AN XY:

135802

show subpopulations

Gnomad AFR exome

AF:

0.292

Gnomad AMR exome

AF:

0.0408

Gnomad ASJ exome

AF:

0.0850

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00928

Gnomad FIN exome

AF:

0.0254

Gnomad NFE exome

AF:

0.0418

Gnomad OTH exome

AF:

0.0530

GnomAD4 exome

AF:

0.0457

AC:

66857

AN:

1461870

Hom.:

2803

Cov.:

AF XY:

0.0441

AC XY:

32093

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.294

Gnomad4 AMR exome

AF:

0.0443

Gnomad4 ASJ exome

AF:

0.0844

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.00931

Gnomad4 FIN exome

AF:

0.0252

Gnomad4 NFE exome

AF:

0.0423

Gnomad4 OTH exome

AF:

0.0555

GnomAD4 genome

AF:

0.108

AC:

16486

AN:

152244

Hom.:

1863

Cov.:

AF XY:

0.104

AC XY:

7714

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.283

Gnomad4 AMR

AF:

0.0648

Gnomad4 ASJ

AF:

0.0905

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.00891

Gnomad4 FIN

AF:

0.0259

Gnomad4 NFE

AF:

0.0419

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.0599

Hom.:

309

Bravo

AF:

0.120

Asia WGS

AF:

0.0390

AC:

137

AN:

3478

EpiCase

AF:

0.0433

EpiControl

AF:

0.0453

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.0020

DANN

Benign

0.44

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