chr9-32449246-T-C

Position:

• chr9-32449246-T-C

Variant summary

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

The NM_002197.3(ACO1):​c.2556+165T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,970 control chromosomes in the GnomAD database, including 23,938 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 0.56 (23938 hom., cov: 31)
• Consequence: ACO1 NM_002197.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACO1	NM_002197.3	c.2556+165T>C		intron_variant		ENST00000309951.8
ACO1	NM_001278352.2	c.2556+165T>C		intron_variant
ACO1	NM_001362840.2	c.2556+165T>C		intron_variant
ACO1	XM_047423430.1	c.2580+165T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACO1	ENST00000309951.8	c.2556+165T>C		intron_variant		1	NM_002197.3	P1
ACO1	ENST00000379923.5	c.2556+165T>C		intron_variant		5		P1
ACO1	ENST00000541043.5	c.2556+165T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85165 AN: 151848 Hom.: 23915 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.561 AC: 85227 AN: 151970 Hom.: 23938 Cov.: 31 AF XY: 0.560 AC XY: 41571 AN XY: 74276

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.555

Alfa AF: 0.570 Hom.: 18508

Bravo AF: 0.557

Asia WGS AF: 0.569 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
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: rs10813818; hg19: chr9-32449244;