3-97971479-G-T

Variant names:

• chr3-97971479-G-T
• rs4857304
• NM_153182.4:c.-40+902C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153182.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIOX2	NM_153182.4	MANE Select	c.-40+902C>A		intron	N/A	NP_694822.2
	RIOX2	NM_001042533.3		c.-40+435C>A		intron	N/A	NP_001035998.1
	RIOX2	NM_001261829.2		c.-40+902C>A		intron	N/A	NP_001248758.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIOX2	ENST00000394198.7	TSL:1 MANE Select	c.-40+902C>A		intron	N/A	ENSP00000377748.2
	RIOX2	ENST00000333396.11	TSL:1	c.-40+435C>A		intron	N/A	ENSP00000328251.6
	RIOX2	ENST00000360258.8	TSL:1	c.-40+435C>A		intron	N/A	ENSP00000353395.4

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

African (AFR) AF: 0.284 AC: 11767 AN: 41444

American (AMR) AF: 0.551 AC: 8425 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1861 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3787 AN: 5170

South Asian (SAS) AF: 0.528 AC: 2549 AN: 4824

European-Finnish (FIN) AF: 0.575 AC: 6069 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35901 AN: 67978

Other (OTH) AF: 0.475 AC: 1001 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.35
PhyloP100		-0.41
PromoterAI		-0.011	Neutral
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: rs4857304; hg19: chr3-97690323;