19-50009254-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000316763.8(VRK3):āc.271T>Cā(p.Ser91Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,614,082 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 (ā ).
Frequency
Consequence
ENST00000316763.8 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VRK3 | NM_016440.4 | c.271T>C | p.Ser91Pro | missense_variant | 4/15 | ENST00000316763.8 | NP_057524.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VRK3 | ENST00000316763.8 | c.271T>C | p.Ser91Pro | missense_variant | 4/15 | 1 | NM_016440.4 | ENSP00000324636 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251314Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135806
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727198
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | 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