chr5-97167551-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018343.3(RIOK2):āc.1313T>Cā(p.Val438Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,900 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 (ā ).
Frequency
Consequence
NM_018343.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RIOK2 | NM_018343.3 | c.1313T>C | p.Val438Ala | missense_variant | 8/10 | ENST00000283109.8 | NP_060813.2 | |
RIOK2 | NM_001159749.2 | c.1313T>C | p.Val438Ala | missense_variant | 8/8 | NP_001153221.1 | ||
RIOK2 | XM_017009628.2 | c.752T>C | p.Val251Ala | missense_variant | 6/8 | XP_016865117.1 | ||
LIX1-AS1 | XR_007058883.1 | n.4605-15457A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIOK2 | ENST00000283109.8 | c.1313T>C | p.Val438Ala | missense_variant | 8/10 | 1 | NM_018343.3 | ENSP00000283109 | P1 | |
LIX1-AS1 | ENST00000504578.2 | n.574-15457A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151954Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251234Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135764
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727222
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.1313T>C (p.V438A) alteration is located in exon 8 (coding exon 8) of the RIOK2 gene. This alteration results from a T to C substitution at nucleotide position 1313, causing the valine (V) at amino acid position 438 to be replaced by an alanine (A). 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