9-32417623-T-G

Variant names:

• chr9-32417623-T-G
• rs10435797
• NM_002197.3:c.405-505T>G

Variant summary

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

The NM_002197.3(ACO1):​c.405-505T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,058 control chromosomes in the GnomAD database, including 8,299 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 (8299 hom., cov: 32)
• Consequence: ACO1 NM_002197.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACO1	NM_002197.3	c.405-505T>G		intron_variant	Intron 4 of 20	ENST00000309951.8	NP_002188.1
ACO1	NM_001278352.2	c.405-505T>G		intron_variant	Intron 5 of 21		NP_001265281.1
ACO1	NM_001362840.2	c.405-505T>G		intron_variant	Intron 5 of 21		NP_001349769.1
ACO1	XM_047423430.1	c.429-505T>G		intron_variant	Intron 4 of 20		XP_047279386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACO1	ENST00000309951.8	c.405-505T>G		intron_variant	Intron 4 of 20	1	NM_002197.3	ENSP00000309477.5
ACO1	ENST00000379923.5	c.405-505T>G		intron_variant	Intron 5 of 21	5		ENSP00000369255.1
ACO1	ENST00000541043.5	c.405-505T>G		intron_variant	Intron 5 of 21	5		ENSP00000438733.2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48991 AN: 151940 Hom.: 8283 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.322 AC: 49037 AN: 152058 Hom.: 8299 Cov.: 32 AF XY: 0.322 AC XY: 23965 AN XY: 74334

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.351

Alfa AF: 0.335 Hom.: 2150

Bravo AF: 0.322

Asia WGS AF: 0.404 AC: 1402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs10435797; hg19: chr9-32417621;