19-1207239-G-T

Variant names:

Variant summary

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

The NM_000455.5(STK11):c.290+36G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,561,928 control chromosomes in the GnomAD database, including 53,360 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5916 hom., cov: 32)

Exomes 𝑓: 0.24 ( 47444 hom. )

Consequence

STK11
NM_000455.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 1.01

Variant links:

Genes affected

STK11 (HGNC:11389): (serine/threonine kinase 11) The protein encoded by this gene is a serine/threonine kinase that regulates cell polarity and energy metabolism and functions as a tumor suppressor. Mutations in this gene have been associated with the autosomal dominant Peutz-Jeghers syndrome, as well as with skin, pancreatic, and testicular cancers. [provided by RefSeq, May 2022]

STK11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 19-1207239-G-T is Benign according to our data. Variant chr19-1207239-G-T is described in ClinVar as [Benign]. Clinvar id is 256203.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1207239-G-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
STK11	NM_000455.5 link	c.290+36G>T	intron_variant	Intron 1 of 9	ENST00000326873.12	NP_000446.1	Q15831-1A0A0S2Z4D1
STK11	NM_001407255.1 link	c.290+36G>T	intron_variant	Intron 1 of 8		NP_001394184.1
STK11	NR_176325.1 link	n.1426+36G>T	intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
STK11	ENST00000326873.12 link	c.290+36G>T	intron_variant	Intron 1 of 9	1	NM_000455.5	ENSP00000324856.6	Q15831-1
STK11	ENST00000652231.1 link	c.290+36G>T	intron_variant	Intron 1 of 8			ENSP00000498804.1	Q15831-2
STK11	ENST00000585748.3 link	c.-82-11178G>T	intron_variant	Intron 3 of 11	3		ENSP00000477641.2	A0A087WT72
STK11	ENST00000593219.5 link	n.290+36G>T	intron_variant	Intron 1 of 3	3		ENSP00000466610.1	K7EMR0

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40211

AN:

151928

Hom.:

5898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.691

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.292

AC:

50356

AN:

172400

Hom.:

8600

AF XY:

0.292

AC XY:

27119

AN XY:

92894

show subpopulations

Gnomad AFR exome

AF:

0.288

Gnomad AMR exome

AF:

0.272

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.687

Gnomad SAS exome

AF:

0.329

Gnomad FIN exome

AF:

0.289

Gnomad NFE exome

AF:

0.227

Gnomad OTH exome

AF:

0.274

GnomAD4 exome

AF:

0.244

AC:

344372

AN:

1409882

Hom.:

47444

Cov.:

AF XY:

0.246

AC XY:

171435

AN XY:

696244

show subpopulations

Gnomad4 AFR exome

AF:

0.284

Gnomad4 AMR exome

AF:

0.267

Gnomad4 ASJ exome

AF:

0.232

Gnomad4 EAS exome

AF:

0.711

Gnomad4 SAS exome

AF:

0.324

Gnomad4 FIN exome

AF:

0.284

Gnomad4 NFE exome

AF:

0.217

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.265

AC:

40278

AN:

152046

Hom.:

5916

Cov.:

AF XY:

0.273

AC XY:

20253

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.282

Gnomad4 AMR

AF:

0.255

Gnomad4 ASJ

AF:

0.225

Gnomad4 EAS

AF:

0.691

Gnomad4 SAS

AF:

0.335

Gnomad4 FIN

AF:

0.284

Gnomad4 NFE

AF:

0.219

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.234

Hom.:

4209

Bravo

AF:

0.266

Asia WGS

AF:

0.497

AC:

1730

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:3

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 02, 2019

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Peutz-Jeghers syndrome

Benign:2

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome

Benign:1

Nov 18, 2014

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.6

DANN

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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