rs863224361
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000455.5(STK11):c.597+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000563 in 1,597,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000455.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK11 | NM_000455.5 | c.597+9G>A | intron_variant | Intron 4 of 9 | ENST00000326873.12 | NP_000446.1 | ||
STK11 | NM_001407255.1 | c.597+9G>A | intron_variant | Intron 4 of 8 | NP_001394184.1 | |||
STK11 | NR_176325.1 | n.1864+9G>A | intron_variant | Intron 5 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STK11 | ENST00000326873.12 | c.597+9G>A | intron_variant | Intron 4 of 9 | 1 | NM_000455.5 | ENSP00000324856.6 | |||
STK11 | ENST00000652231.1 | c.597+9G>A | intron_variant | Intron 4 of 8 | ENSP00000498804.1 | |||||
STK11 | ENST00000585748.3 | c.225+9G>A | intron_variant | Intron 6 of 11 | 3 | ENSP00000477641.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000455 AC: 1AN: 219812Hom.: 0 AF XY: 0.00000834 AC XY: 1AN XY: 119876
GnomAD4 exome AF: 0.00000415 AC: 6AN: 1445120Hom.: 0 Cov.: 32 AF XY: 0.00000279 AC XY: 2AN XY: 717218
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Variant summary: STK11 c.597+9G>A alters a non-conserved nucleotide located at a position not widely known to affect splicing. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4.5e-06 in 219812 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.597+9G>A in individuals affected with Peutz-Jeghers Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign. -
Peutz-Jeghers syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at