rs316191

chr5-97171923-A-Cchr5-97171923-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018343.3(RIOK2):c.588-526T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,942 control chromosomes in the GnomAD database, including 10,139 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (10139 hom., cov: 31)
• Consequence: RIOK2 NM_018343.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

Genes affected

RIOK2 (HGNC:18999): (RIO kinase 2) Predicted to enable protein kinase activity. Involved in several processes, including positive regulation of rRNA processing; positive regulation of ribosomal small subunit export from nucleus; and regulation of mitotic metaphase/anaphase transition. Located in cytoplasm. Part of preribosome, small subunit precursor. [provided by Alliance of Genome Resources, Apr 2022]

LIX1-AS1 (HGNC:52976): (LIX1 and RIOK2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIOK2	NM_018343.3	c.588-526T>G		intron_variant		ENST00000283109.8
RIOK2	NM_001159749.2	c.588-526T>G		intron_variant
RIOK2	XM_017009628.2	c.27-526T>G		intron_variant
LIX1-AS1	XR_007058883.1	n.4605-11085A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIOK2	ENST00000283109.8	c.588-526T>G		intron_variant		1	NM_018343.3	P1
RIOK2	ENST00000508447.1	c.588-526T>G		intron_variant		1
LIX1-AS1	ENST00000504578.2	n.574-11085A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51474 AN: 151824 Hom.: 10130 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.310

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.339 AC: 51502 AN: 151942 Hom.: 10139 Cov.: 31 AF XY: 0.345 AC XY: 25596 AN XY: 74270

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.309

Alfa AF: 0.306 Hom.: 1306

Bravo AF: 0.319

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs316191; hg19: chr5-96507627;