6-31972449-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004197.2(STK19):c.38T>C(p.Phe13Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,612,876 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK19 | NM_004197.2 | c.38T>C | p.Phe13Ser | missense_variant | 1/7 | ENST00000685781.1 | |
STK19 | NM_032454.1 | c.368T>C | p.Phe123Ser | missense_variant | 2/8 | ||
STK19 | NR_026717.1 | n.681T>C | non_coding_transcript_exon_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK19 | ENST00000685781.1 | c.38T>C | p.Phe13Ser | missense_variant | 1/7 | NM_004197.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247408Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134716
GnomAD4 exome AF: 0.0000548 AC: 80AN: 1460764Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 726698
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.368T>C (p.F123S) alteration is located in exon 2 (coding exon 2) of the STK19 gene. This alteration results from a T to C substitution at nucleotide position 368, causing the phenylalanine (F) at amino acid position 123 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