6-7393142-C-T

Variant names:

• chr6-7393142-C-T
• NM_031480.3:c.115C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_001348194.2(RIOK1):​c.-230C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RIOK1 NM_001348194.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.437
• Publications: 0 publications found

Genes affected

RIOK1 (HGNC:18656): (RIO kinase 1) The protein encoded by this gene competes with pICln for inclusion in the protein arginine methyltransferase 5 complex. This complex targets substrates for dimethylation. The encoded protein is essential for the last steps in the maturation of 40S subunits. [provided by RefSeq, Jan 2017]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 6-7393142-C-T is Benign according to our data. Variant chr6-7393142-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2656207.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348194.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIOK1	NM_031480.3	MANE Select	c.115C>T	p.Leu39Leu	synonymous	Exon 2 of 17	NP_113668.2
	RIOK1	NM_001348194.2		c.-230C>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 17	NP_001335123.1
	RIOK1	NM_001348194.2		c.-230C>T		5_prime_UTR	Exon 2 of 17	NP_001335123.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIOK1	ENST00000379834.7	TSL:1 MANE Select	c.115C>T	p.Leu39Leu	synonymous	Exon 2 of 17	ENSP00000369162.2	Q9BRS2
	RIOK1	ENST00000475351.5	TSL:1	n.115C>T		non_coding_transcript_exon	Exon 2 of 8	ENSP00000418263.1	E9PFQ8
	RIOK1	ENST00000967571.1		c.115C>T	p.Leu39Leu	synonymous	Exon 2 of 18	ENSP00000637630.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.60
PhyloP100		-0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

hg19: chr6-7393375;