6-31979423-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004197.2(STK19):c.343G>T(p.Ala115Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,612,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004197.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK19 | NM_004197.2 | c.343G>T | p.Ala115Ser | missense_variant | 4/7 | ENST00000685781.1 | |
STK19 | NM_032454.1 | c.685G>T | p.Ala229Ser | missense_variant | 5/8 | ||
STK19 | NR_026717.1 | n.986G>T | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK19 | ENST00000685781.1 | c.343G>T | p.Ala115Ser | missense_variant | 4/7 | NM_004197.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151992Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246558Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134394
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460736Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726682
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151992Hom.: 0 Cov.: 29 AF XY: 0.0000135 AC XY: 1AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2022 | The c.685G>T (p.A229S) alteration is located in exon 5 (coding exon 5) of the STK19 gene. This alteration results from a G to T substitution at nucleotide position 685, causing the alanine (A) at amino acid position 229 to be replaced by a serine (S). 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