rs730881960
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_000455.5(STK11):c.464+20del 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 made for transcript
Verdict is Benign. Variant got -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. gnomad4_exome 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 gnomad4_exome. There are 30 alleles in male gnomad4_exome subpopulation. Median coverage is 45. This position pass quality control queck.
BS2
?
High AC in GnomAdExome4 at 75 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK11 | NM_000455.5 | c.464+20del | intron_variant | ENST00000326873.12 | |||
STK11 | NM_001407255.1 | c.464+20del | intron_variant | ||||
STK11 | NR_176325.1 | n.1731+20del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK11 | ENST00000326873.12 | c.464+20del | intron_variant | 1 | NM_000455.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000216 AC: 3AN: 138678Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000376 AC: 64AN: 170296Hom.: 1 AF XY: 0.000317 AC XY: 29AN XY: 91418
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GnomAD4 exome AF: 0.000103 AC: 75AN: 726494Hom.: 1 Cov.: 45 AF XY: 0.0000810 AC XY: 30AN XY: 370290
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GnomAD4 genome ? AF: 0.0000216 AC: 3AN: 138678Hom.: 0 Cov.: 34 AF XY: 0.0000149 AC XY: 1AN XY: 67234
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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
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Counsyl | Sep 06, 2016 | - - |
Hereditary cancer-predisposing syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Aug 31, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 21, 2014 | The variant is found in HEREDICANCER,BR-OV-HEREDIC panel(s). - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 20, 2017 | - - |
Computational scores
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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