chr19-1226441-G-T

Variant names:

• chr19-1226441-G-T
• rs568152768
• NM_000455.5:c.1109-13G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 2P and 12B. PM2 BP4_Strong BP6_Very_Strong

The NM_000455.5(STK11):​c.1109-13G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: STK11 NM_000455.5 intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.36
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• familial pancreatic carcinoma

  Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
• Peutz-Jeghers syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, Genomics England PanelApp, G2P
• familial ovarian cancer

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 19-1226441-G-T is Benign according to our data. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-1226441-G-T is described in CliVar as Likely_benign. Clinvar id is 388813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK11	NM_000455.5	c.1109-13G>T		intron_variant	Intron 8 of 9	ENST00000326873.12	NP_000446.1
STK11	NR_176325.1	n.2376-13G>T		intron_variant	Intron 9 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK11	ENST00000326873.12	c.1109-13G>T		intron_variant	Intron 8 of 9	1	NM_000455.5	ENSP00000324856.6
STK11	ENST00000585748.3	c.737-13G>T		intron_variant	Intron 10 of 11	3		ENSP00000477641.2
STK11	ENST00000593219.6	n.*934-13G>T		intron_variant	Intron 9 of 10	3		ENSP00000466610.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Aug 22, 2016

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Peutz-Jeghers syndrome Benign:1

Jun 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.10
DANN	Benign	0.79
PhyloP100		-2.4

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

Other links and lift over

dbSNP: rs568152768; hg19: chr19-1226440;