rs316191

Variant names:

• chr5-97171923-A-C
• rs316191
• NM_018343.3:c.588-526T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-97171923-A-C
• chr5-97171923-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RIOK2	NM_018343.3	c.588-526T>G		intron_variant	Intron 5 of 9	ENST00000283109.8	NP_060813.2
RIOK2	NM_001159749.2	c.588-526T>G		intron_variant	Intron 5 of 7		NP_001153221.1
RIOK2	XM_017009628.2	c.27-526T>G		intron_variant	Intron 3 of 7		XP_016865117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIOK2	ENST00000283109.8	c.588-526T>G		intron_variant	Intron 5 of 9	1	NM_018343.3	ENSP00000283109.3
RIOK2	ENST00000508447.1	c.588-526T>G		intron_variant	Intron 5 of 7	1		ENSP00000420932.1
LIX1-AS1	ENST00000504578.2	n.574-11085A>C		intron_variant	Intron 3 of 6	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

African (AFR) AF: 0.134 AC: 5562 AN: 41482

American (AMR) AF: 0.408 AC: 6221 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1188 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2395 AN: 5150

South Asian (SAS) AF: 0.413 AC: 1987 AN: 4810

European-Finnish (FIN) AF: 0.504 AC: 5314 AN: 10534

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27908 AN: 67918

Other (OTH) AF: 0.309 AC: 652 AN: 2108

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
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs316191; hg19: chr5-96507627;