rs786201097
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_000455.5(STK11):c.846C>T(p.Leu282Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L282L) has been classified as Benign.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Consequence
STK11
NM_000455.5 synonymous
NM_000455.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.36
Publications
2 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 carcinomaInheritance: AD Classification: DEFINITIVE Submitted by: G2P
- Peutz-Jeghers syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, Genomics England PanelApp, G2P
- familial ovarian cancerInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 19-1221324-C-T is Benign according to our data. Variant chr19-1221324-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 628828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.36 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000455.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| STK11 | NM_000455.5 | MANE Select | c.846C>T | p.Leu282Leu | synonymous | Exon 6 of 10 | NP_000446.1 | ||
| STK11 | NM_001407255.1 | c.846C>T | p.Leu282Leu | synonymous | Exon 6 of 9 | NP_001394184.1 | |||
| STK11 | NR_176325.1 | n.2113C>T | non_coding_transcript_exon | Exon 7 of 11 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| STK11 | ENST00000326873.12 | TSL:1 MANE Select | c.846C>T | p.Leu282Leu | synonymous | Exon 6 of 10 | ENSP00000324856.6 | ||
| STK11 | ENST00000652231.1 | c.846C>T | p.Leu282Leu | synonymous | Exon 6 of 9 | ENSP00000498804.1 | |||
| STK11 | ENST00000585748.3 | TSL:3 | c.474C>T | p.Leu158Leu | synonymous | Exon 8 of 12 | ENSP00000477641.2 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152242
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152242
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74370
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41464
American (AMR)
AF:
AC:
0
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5202
South Asian (SAS)
AF:
AC:
0
AN:
4836
European-Finnish (FIN)
AF:
AC:
0
AN:
10632
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
2
AN:
68026
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
Significance:Benign/Likely benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
2
Hereditary cancer-predisposing syndrome (2)
-
-
2
Peutz-Jeghers syndrome (2)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.