19-1218444-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000455.5(STK11):c.318G>T(p.Arg106Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,308 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. R106R) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
STK11
NM_000455.5 synonymous
NM_000455.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.50
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 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
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 19-1218444-G-T is Benign according to our data. Variant chr19-1218444-G-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 233125.
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.318G>T | p.Arg106Arg | synonymous | Exon 2 of 10 | NP_000446.1 | ||
| STK11 | NM_001407255.1 | c.318G>T | p.Arg106Arg | synonymous | Exon 2 of 9 | NP_001394184.1 | |||
| STK11 | NR_176325.1 | n.1585G>T | non_coding_transcript_exon | Exon 3 of 11 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| STK11 | ENST00000326873.12 | TSL:1 MANE Select | c.318G>T | p.Arg106Arg | synonymous | Exon 2 of 10 | ENSP00000324856.6 | ||
| STK11 | ENST00000652231.1 | c.318G>T | p.Arg106Arg | synonymous | Exon 2 of 9 | ENSP00000498804.1 | |||
| STK11 | ENST00000593219.6 | TSL:3 | n.*143G>T | non_coding_transcript_exon | Exon 3 of 11 | ENSP00000466610.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00000401 AC: 1AN: 249166 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
249166
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461308Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726920 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461308
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
726920
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33478
American (AMR)
AF:
AC:
0
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
1
AN:
39698
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53126
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111772
Other (OTH)
AF:
AC:
0
AN:
60358
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
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2
0.00
0.20
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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<30
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
Significance:Conflicting classifications of pathogenicity
Revision:criteria provided, conflicting classifications
Pathogenic
VUS
Benign
Condition
-
-
3
Peutz-Jeghers syndrome (3)
-
-
2
Hereditary cancer-predisposing syndrome (2)
-
-
2
not specified (2)
-
-
1
Breast and/or ovarian cancer (1)
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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
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