19-1209715-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000455.5(STK11):​c.290+2512C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,940 control chromosomes in the GnomAD database, including 22,805 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 22805 hom., cov: 31)

Consequence

STK11
NM_000455.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.488
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STK11NM_000455.5 linkc.290+2512C>G intron_variant Intron 1 of 9 ENST00000326873.12 NP_000446.1 Q15831-1A0A0S2Z4D1
STK11NM_001407255.1 linkc.290+2512C>G intron_variant Intron 1 of 8 NP_001394184.1
STK11NR_176325.1 linkn.1426+2512C>G intron_variant Intron 1 of 10

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STK11ENST00000326873.12 linkc.290+2512C>G intron_variant Intron 1 of 9 1 NM_000455.5 ENSP00000324856.6 Q15831-1
STK11ENST00000652231.1 linkc.290+2512C>G intron_variant Intron 1 of 8 ENSP00000498804.1 Q15831-2
STK11ENST00000585748.3 linkc.-82-8702C>G intron_variant Intron 3 of 11 3 ENSP00000477641.2 A0A087WT72
STK11ENST00000593219.5 linkn.290+2512C>G intron_variant Intron 1 of 3 3 ENSP00000466610.1 K7EMR0

Frequencies

GnomAD3 genomes
AF:
0.536
AC:
81308
AN:
151822
Hom.:
22769
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.630
Gnomad AMI
AF:
0.501
Gnomad AMR
AF:
0.513
Gnomad ASJ
AF:
0.425
Gnomad EAS
AF:
0.982
Gnomad SAS
AF:
0.624
Gnomad FIN
AF:
0.481
Gnomad MID
AF:
0.525
Gnomad NFE
AF:
0.458
Gnomad OTH
AF:
0.528
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.536
AC:
81410
AN:
151940
Hom.:
22805
Cov.:
31
AF XY:
0.543
AC XY:
40291
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.630
Gnomad4 AMR
AF:
0.513
Gnomad4 ASJ
AF:
0.425
Gnomad4 EAS
AF:
0.982
Gnomad4 SAS
AF:
0.624
Gnomad4 FIN
AF:
0.481
Gnomad4 NFE
AF:
0.458
Gnomad4 OTH
AF:
0.534
Alfa
AF:
0.334
Hom.:
832
Bravo
AF:
0.540
Asia WGS
AF:
0.798
AC:
2772
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
6.9
DANN
Benign
0.71
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8111699; hg19: chr19-1209714; API