3-97971479-G-T

Position:

• chr3-97971479-G-T

Variant summary

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

The NM_153182.4(RIOX2):​c.-40+902C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,034 control chromosomes in the GnomAD database, including 18,237 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 0.47 (18237 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: RIOX2 NM_153182.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

Genes affected

RIOX2 (HGNC:19441): (ribosomal oxygenase 2) MINA is a c-Myc (MYC; MIM 190080) target gene that may play a role in cell proliferation or regulation of cell growth. (Tsuneoka et al., 2002 [PubMed 12091391]; Zhang et al., 2005 [PubMed 15897898]).[supplied by OMIM, May 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RIOX2	NM_153182.4	c.-40+902C>A		intron_variant		ENST00000394198.7	NP_694822.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIOX2	ENST00000394198.7	c.-40+902C>A		intron_variant		1	NM_153182.4	ENSP00000377748	P3
RIOX2	ENST00000333396.11	c.-40+435C>A		intron_variant		1		ENSP00000328251	P3
RIOX2	ENST00000360258.8	c.-40+435C>A		intron_variant		1		ENSP00000353395	A1
RIOX2	ENST00000506099.1	c.-40+111C>A		intron_variant		4		ENSP00000423816

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72090 AN: 151916 Hom.: 18227 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.474 AC: 72114 AN: 152034 Hom.: 18237 Cov.: 33 AF XY: 0.480 AC XY: 35701 AN XY: 74332

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.475

Alfa AF: 0.372 Hom.: 1285

Bravo AF: 0.463

Asia WGS AF: 0.619 AC: 2150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.35

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: rs4857304; hg19: chr3-97690323;