chr6-31978936-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004197.2(STK19):c.271G>A(p.Val91Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,612,490 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 Likely benign (★).
Frequency
Consequence
NM_004197.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK19 | NM_004197.2 | c.271G>A | p.Val91Ile | missense_variant | 3/7 | ENST00000685781.1 | |
STK19 | NM_032454.1 | c.601G>A | p.Val201Ile | missense_variant | 4/8 | ||
STK19 | NR_026717.1 | n.914G>A | non_coding_transcript_exon_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK19 | ENST00000685781.1 | c.271G>A | p.Val91Ile | missense_variant | 3/7 | NM_004197.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151780Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000487 AC: 12AN: 246518Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134384
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460710Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 726668
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151780Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74102
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2023 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at