GeneBe

rs730881964

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000455.5(STK11):​c.920+6C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

STK11
NM_000455.5 splice_region, intron

Scores

2
Splicing: ADA: 0.0003145
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0420

Publications

1 publications found
Variant links:
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 carcinoma
    Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
  • Peutz-Jeghers syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, Genomics England PanelApp, G2P
  • familial ovarian cancer
    Inheritance: 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 -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).

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
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
STK11
NM_000455.5
MANE Select
c.920+6C>A
splice_region intron
N/ANP_000446.1
STK11
NM_001407255.1
c.920+6C>A
splice_region intron
N/ANP_001394184.1
STK11
NR_176325.1
n.2187+6C>A
splice_region intron
N/A

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
STK11
ENST00000326873.12
TSL:1 MANE Select
c.920+6C>A
splice_region intron
N/AENSP00000324856.6
STK11
ENST00000652231.1
c.920+6C>A
splice_region intron
N/AENSP00000498804.1
STK11
ENST00000585748.3
TSL:3
c.548+6C>A
splice_region intron
N/AENSP00000477641.2

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1415470
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
700118
African (AFR)
AF:
0.00
AC:
0
AN:
32232
American (AMR)
AF:
0.00
AC:
0
AN:
38272
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25390
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36810
South Asian (SAS)
AF:
0.00
AC:
0
AN:
80466
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48758
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5718
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1089224
Other (OTH)
AF:
0.00
AC:
0
AN:
58600
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
3.0
DANN
Benign
0.85
PhyloP100
-0.042
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00031
dbscSNV1_RF
Benign
0.024
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs730881964; hg19: chr19-1222011; API