chr8-98526778-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_006281.4(STK3):c.1281T>A(p.Asp427Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000221 in 1,583,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006281.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK3 | NM_006281.4 | c.1281T>A | p.Asp427Glu | missense_variant | 10/11 | ENST00000419617.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK3 | ENST00000419617.7 | c.1281T>A | p.Asp427Glu | missense_variant | 10/11 | 1 | NM_006281.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000846 AC: 2AN: 236454Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128064
GnomAD4 exome AF: 0.0000230 AC: 33AN: 1431726Hom.: 0 Cov.: 30 AF XY: 0.0000211 AC XY: 15AN XY: 710480
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2022 | The c.1281T>A (p.D427E) alteration is located in exon 10 (coding exon 10) of the STK3 gene. This alteration results from a T to A substitution at nucleotide position 1281, causing the aspartic acid (D) at amino acid position 427 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at