NM_000455.5:c.1167C>T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000455.5(STK11):c.1167C>T(p.Ala389Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000617 in 1,458,194 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 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK11 | NM_000455.5 | c.1167C>T | p.Ala389Ala | synonymous_variant | Exon 9 of 10 | ENST00000326873.12 | NP_000446.1 | |
STK11 | NR_176325.1 | n.2434C>T | non_coding_transcript_exon_variant | Exon 10 of 11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STK11 | ENST00000326873.12 | c.1167C>T | p.Ala389Ala | synonymous_variant | Exon 9 of 10 | 1 | NM_000455.5 | ENSP00000324856.6 | ||
STK11 | ENST00000585748.3 | c.795C>T | p.Ala265Ala | synonymous_variant | Exon 11 of 12 | 3 | ENSP00000477641.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000417 AC: 1AN: 239662Hom.: 0 AF XY: 0.00000760 AC XY: 1AN XY: 131552
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1458194Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 4AN XY: 725240
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Peutz-Jeghers syndrome Benign:3
- -
- -
- -
Hereditary cancer-predisposing syndrome Benign:2
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
- -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at