rs13293491

chr9-32425272-G-Achr9-32425272-G-C

Variant summary

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

The NM_002197.3(ACO1):c.1189-566G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,090 control chromosomes in the GnomAD database, including 8,061 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 0.32 (8061 hom., cov: 33)
• Consequence: ACO1 NM_002197.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

ACO1 (HGNC:117): (aconitase 1) The protein encoded by this gene is a bifunctional, cytosolic protein that functions as an essential enzyme in the TCA cycle and interacts with mRNA to control the levels of iron inside cells. When cellular iron levels are high, this protein binds to a 4Fe-4S cluster and functions as an aconitase. Aconitases are iron-sulfur proteins that function to catalyze the conversion of citrate to isocitrate. When cellular iron levels are low, the protein binds to iron-responsive elements (IREs), which are stem-loop structures found in the 5' UTR of ferritin mRNA, and in the 3' UTR of transferrin receptor mRNA. When the protein binds to IRE, it results in repression of translation of ferritin mRNA, and inhibition of degradation of the otherwise rapidly degraded transferrin receptor mRNA. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. Alternative splicing results in multiple transcript variants [provided by RefSeq, Jan 2014]

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 = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACO1	NM_002197.3	c.1189-566G>A		intron_variant		ENST00000309951.8
ACO1	NM_001278352.2	c.1189-566G>A		intron_variant
ACO1	NM_001362840.2	c.1189-566G>A		intron_variant
ACO1	XM_047423430.1	c.1213-566G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACO1	ENST00000309951.8	c.1189-566G>A		intron_variant		1	NM_002197.3	P1
ACO1	ENST00000379923.5	c.1189-566G>A		intron_variant		5		P1
ACO1	ENST00000541043.5	c.1189-566G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48137 AN: 151972 Hom.: 8055 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.317 AC: 48162 AN: 152090 Hom.: 8061 Cov.: 33 AF XY: 0.317 AC XY: 23561 AN XY: 74368

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.351

Alfa AF: 0.345 Hom.: 9513

Bravo AF: 0.315

Asia WGS AF: 0.402 AC: 1395 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	3.6
Dann	Benign	0.42

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: rs13293491; hg19: chr9-32425270;