chr19-1219429-AG-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_000455.5(STK11):c.464+20delG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000902 in 865,172 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000022 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00010 ( 1 hom. )
Consequence
STK11
NM_000455.5 intron
NM_000455.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.124
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -16 ACMG points.
BP6
Variant 19-1219429-AG-A is Benign according to our data. Variant chr19-1219429-AG-A is described in ClinVar as [Likely_benign]. Clinvar id is 182879.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population amr. GnomAdExome4 allele frequency = 0.000103 (75/726494) while in subpopulation AMR AF = 0.00222 (68/30670). AF 95% confidence interval is 0.00179. There are 1 homozygotes in GnomAdExome4. There are 30 alleles in the male GnomAdExome4 subpopulation. Median coverage is 45. This position FAILED quality control check.
BS2
High AC in GnomAdExome4 at 75 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK11 | NM_000455.5 | c.464+20delG | intron_variant | Intron 3 of 9 | ENST00000326873.12 | NP_000446.1 | ||
STK11 | NM_001407255.1 | c.464+20delG | intron_variant | Intron 3 of 8 | NP_001394184.1 | |||
STK11 | NR_176325.1 | n.1731+20delG | intron_variant | Intron 4 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STK11 | ENST00000326873.12 | c.464+17delG | intron_variant | Intron 3 of 9 | 1 | NM_000455.5 | ENSP00000324856.6 | |||
STK11 | ENST00000652231.1 | c.464+17delG | intron_variant | Intron 3 of 8 | ENSP00000498804.1 | |||||
STK11 | ENST00000585748.3 | c.92+17delG | intron_variant | Intron 5 of 11 | 3 | ENSP00000477641.2 | ||||
STK11 | ENST00000593219.5 | n.*306delG | downstream_gene_variant | 3 | ENSP00000466610.1 |
Frequencies
GnomAD3 genomes AF: 0.0000216 AC: 3AN: 138678Hom.: 0 Cov.: 34 show subpopulations
GnomAD3 genomes
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3
AN:
138678
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Cov.:
34
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GnomAD2 exomes AF: 0.000376 AC: 64AN: 170296 AF XY: 0.000317 show subpopulations
GnomAD2 exomes
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64
AN:
170296
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GnomAD4 exome AF: 0.000103 AC: 75AN: 726494Hom.: 1 Cov.: 45 AF XY: 0.0000810 AC XY: 30AN XY: 370290 show subpopulations
GnomAD4 exome
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75
AN:
726494
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45
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30
AN XY:
370290
Gnomad4 AFR exome
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0
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17146
Gnomad4 AMR exome
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68
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30670
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0
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14226
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0
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13836
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0
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68672
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0
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29424
Gnomad4 NFE exome
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1
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520718
Gnomad4 Remaining exome
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AC:
6
AN:
28490
Heterozygous variant carriers
0
6
11
17
22
28
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0.95
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GnomAD4 genome AF: 0.0000216 AC: 3AN: 138678Hom.: 0 Cov.: 34 AF XY: 0.0000149 AC XY: 1AN XY: 67234 show subpopulations
GnomAD4 genome
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AC:
3
AN:
138678
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Cov.:
34
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1
AN XY:
67234
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0
Gnomad4 AMR
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0.000142491
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0.000142491
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0.0000155972
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0.0000155972
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0
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0
Heterozygous variant carriers
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1
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Allele balance
Genome Het
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Peutz-Jeghers syndrome Benign:3
Sep 06, 2016
Counsyl
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Jul 15, 2021
Genome-Nilou Lab
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Feb 02, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Hereditary cancer-predisposing syndrome Benign:2
Aug 31, 2016
Color Diagnostics, LLC DBA Color Health
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Aug 21, 2014
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
The variant is found in HEREDICANCER,BR-OV-HEREDIC panel(s). -
not specified Benign:1
Dec 20, 2017
PreventionGenetics, part of Exact Sciences
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
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Prediction
Mutation Taster
=100/0
polymorphism
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at