rs2232873

Variant names:

• chr22-50486669-G-A
• rs2232873
• NM_017584.6:c.-229G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-50486669-G-A
• chr22-50486669-G-C

Variant summary

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

The NM_017584.6(MIOX):​c.-229G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 623,754 control chromosomes in the GnomAD database, including 11,561 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 0.17 (3124 hom., cov: 33)
  • Exomes 𝑓: 0.15 (8437 hom.)
• Consequence: MIOX NM_017584.6 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

MIOX (HGNC:14522): (myo-inositol oxygenase) Enables ferric iron binding activity and inositol oxygenase activity. Involved in inositol catabolic process. Predicted to be located in cytoplasm and inclusion body. [provided by Alliance of Genome Resources, Apr 2022]

ADM2 (HGNC:28898): (adrenomedullin 2) This gene encodes a member of the calcitonin gene-related peptide (CGRP)/calcitonin family of hormones that play a role in the regulation of cardiovascular homeostasis, prolactin release, anti-diuresis, anti-natriuresis, and regulation of food and water intake. The encoded protein is proteolytically processed to generate one or more biologically active peptides. [provided by RefSeq, Jul 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIOX	NM_017584.6	c.-229G>A		upstream_gene_variant		ENST00000216075.11	NP_060054.4
ADM2	NM_001253845.2	c.*3766G>A		downstream_gene_variant		ENST00000395737.2	NP_001240774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIOX	ENST00000216075.11	c.-229G>A		upstream_gene_variant		1	NM_017584.6	ENSP00000216075.6
ADM2	ENST00000395737.2	c.*3766G>A		downstream_gene_variant		1	NM_001253845.2	ENSP00000379086.1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26307 AN: 152060 Hom.: 3114 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.151 AC: 71257 AN: 471576 Hom.: 8437 AF XY: 0.157 AC XY: 39309 AN XY: 250182

Gnomad4 AFR exome AF: 0.244

Gnomad4 AMR exome AF: 0.307

Gnomad4 ASJ exome AF: 0.186

Gnomad4 EAS exome AF: 0.392

Gnomad4 SAS exome AF: 0.299

Gnomad4 FIN exome AF: 0.141

Gnomad4 NFE exome AF: 0.0776

Gnomad4 OTH exome AF: 0.159

GnomAD4 genome AF: 0.173 AC: 26342 AN: 152178 Hom.: 3124 Cov.: 33 AF XY: 0.186 AC XY: 13803 AN XY: 74404

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.194

Alfa AF: 0.102 Hom.: 1330

Bravo AF: 0.184

Asia WGS AF: 0.339 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2232873; hg19: chr22-50925098; COSMIC: COSV53315000;