ENST00000585748:c.-259T>G

Variant names:

• chr19-1189483-T-G
• rs9304882
• ENST00000585748:c.-259T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000585748(STK11):​c.-259T>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,270 control chromosomes in the GnomAD database, including 5,163 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 0.25 (5158 hom., cov: 32)
  • Exomes 𝑓: 0.29 (5 hom.)
• Consequence: STK11 ENST00000585748 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK11	ENST00000585748	c.-259T>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 3 of 12	3		ENSP00000477641.2
STK11	ENST00000585748	c.-259T>G		5_prime_UTR_variant	Exon 3 of 12	3		ENSP00000477641.2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38574 AN: 152054 Hom.: 5143 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.286 AC: 28 AN: 98 Hom.: 5 Cov.: 0 AF XY: 0.270 AC XY: 20 AN XY: 74

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.700

Gnomad4 NFE exome AF: 0.243

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.254 AC: 38636 AN: 152172 Hom.: 5158 Cov.: 32 AF XY: 0.247 AC XY: 18388 AN XY: 74404

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0332

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.231

Alfa AF: 0.263 Hom.: 11132

Bravo AF: 0.245

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9304882; hg19: chr19-1189482;