NM_018343.3:c.1021G>T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018343.3(RIOK2):c.1021G>T(p.Val341Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018343.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RIOK2 | NM_018343.3 | c.1021G>T | p.Val341Leu | missense_variant | Exon 8 of 10 | ENST00000283109.8 | NP_060813.2 | |
RIOK2 | NM_001159749.2 | c.1021G>T | p.Val341Leu | missense_variant | Exon 8 of 8 | NP_001153221.1 | ||
RIOK2 | XM_017009628.2 | c.460G>T | p.Val154Leu | missense_variant | Exon 6 of 8 | XP_016865117.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIOK2 | ENST00000283109.8 | c.1021G>T | p.Val341Leu | missense_variant | Exon 8 of 10 | 1 | NM_018343.3 | ENSP00000283109.3 | ||
RIOK2 | ENST00000508447.1 | c.1021G>T | p.Val341Leu | missense_variant | Exon 8 of 8 | 1 | ENSP00000420932.1 | |||
LIX1-AS1 | ENST00000504578.2 | n.574-15165C>A | intron_variant | Intron 3 of 6 | 5 | |||||
RIOK2 | ENST00000511012.1 | c.-126G>T | upstream_gene_variant | 2 | ENSP00000422772.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461612Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 727108 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1021G>T (p.V341L) alteration is located in exon 8 (coding exon 8) of the RIOK2 gene. This alteration results from a G to T substitution at nucleotide position 1021, causing the valine (V) at amino acid position 341 to be replaced by a leucine (L). 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