rs730881962
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_000455.5(STK11):c.734+19delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000828 in 1,448,820 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000083 ( 0 hom. )
Consequence
STK11
NM_000455.5 intron
NM_000455.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00600
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: Likely_benign. The variant received -2 ACMG points.
BP6
Variant 19-1220729-GC-G is Benign according to our data. Variant chr19-1220729-GC-G is described in ClinVar as Benign. ClinVar VariationId is 1600558.Status of the report is criteria_provided_single_submitter, 1 stars.
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.734+19delC | intron | N/A | NP_000446.1 | |||
| STK11 | NM_001407255.1 | c.734+19delC | intron | N/A | NP_001394184.1 | ||||
| STK11 | NR_176325.1 | n.2001+19delC | intron | N/A |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| STK11 | ENST00000326873.12 | TSL:1 MANE Select | c.734+13delC | intron | N/A | ENSP00000324856.6 | |||
| STK11 | ENST00000652231.1 | c.734+13delC | intron | N/A | ENSP00000498804.1 | ||||
| STK11 | ENST00000585748.3 | TSL:3 | c.362+13delC | intron | N/A | ENSP00000477641.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.0000173 AC: 4AN: 230910 AF XY: 0.0000236 show subpopulations
GnomAD2 exomes
AF:
AC:
4
AN:
230910
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: 0.00000828 AC: 12AN: 1448820Hom.: 0 Cov.: 32 AF XY: 0.0000139 AC XY: 10AN XY: 719392 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
12
AN:
1448820
Hom.:
Cov.:
32
AF XY:
AC XY:
10
AN XY:
719392
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
33202
American (AMR)
AF:
AC:
0
AN:
44096
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
25634
East Asian (EAS)
AF:
AC:
0
AN:
39484
South Asian (SAS)
AF:
AC:
1
AN:
85362
European-Finnish (FIN)
AF:
AC:
2
AN:
51618
Middle Eastern (MID)
AF:
AC:
0
AN:
4590
European-Non Finnish (NFE)
AF:
AC:
8
AN:
1105186
Other (OTH)
AF:
AC:
0
AN:
59648
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000000185555), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.304
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions as Germline
Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Peutz-Jeghers syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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
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