chr3-97951833-G-A

Variant names:

• chr3-97951833-G-A
• rs1532206
• NM_153182.4:c.786-945C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153182.4(RIOX2):​c.786-945C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,082 control chromosomes in the GnomAD database, including 7,729 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 0.30 (7729 hom., cov: 32)
• Consequence: RIOX2 NM_153182.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIOX2	NM_153182.4	c.786-945C>T		intron_variant	Intron 5 of 9	ENST00000394198.7	NP_694822.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIOX2	ENST00000394198.7	c.786-945C>T		intron_variant	Intron 5 of 9	1	NM_153182.4	ENSP00000377748.2
RIOX2	ENST00000333396.11	c.786-945C>T		intron_variant	Intron 5 of 9	1		ENSP00000328251.6
RIOX2	ENST00000360258.8	c.786-945C>T		intron_variant	Intron 5 of 9	1		ENSP00000353395.4
RIOX2	ENST00000514314.5	n.*43+319C>T		intron_variant	Intron 5 of 7	1		ENSP00000424955.1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46277 AN: 151964 Hom.: 7720 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.304 AC: 46300 AN: 152082 Hom.: 7729 Cov.: 32 AF XY: 0.309 AC XY: 22930 AN XY: 74326

African (AFR) AF: 0.171 AC: 7087 AN: 41510

American (AMR) AF: 0.344 AC: 5251 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1521 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2686 AN: 5150

South Asian (SAS) AF: 0.348 AC: 1678 AN: 4818

European-Finnish (FIN) AF: 0.354 AC: 3737 AN: 10564

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23181 AN: 67980

Other (OTH) AF: 0.324 AC: 683 AN: 2110

Alfa AF: 0.334 Hom.: 6332

Bravo AF: 0.302

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.3
DANN	Benign	0.68
PhyloP100		0.30
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: rs1532206; hg19: chr3-97670677;