chr13-76948790-T-C

Variant names:

• chr13-76948790-T-C
• rs588702
• NM_001258406.2:c.12+220T>C

Variant summary

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

The NM_001258406.2(ACOD1):​c.12+220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 152,192 control chromosomes in the GnomAD database, including 50,703 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 0.81 (50703 hom., cov: 32)
• Consequence: ACOD1 NM_001258406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 3 publications found

Genes affected

ACOD1 (HGNC:33904): (aconitate decarboxylase 1) Enables aconitate decarboxylase activity. Involved in defense response; positive regulation of antimicrobial humoral response; and tolerance induction to lipopolysaccharide. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000307967 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258406.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOD1	NM_001258406.2	MANE Select	c.12+220T>C		intron	N/A	NP_001245335.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOD1	ENST00000377462.6	TSL:5 MANE Select	c.12+220T>C		intron	N/A	ENSP00000366682.1
	ENSG00000307967	ENST00000830114.1		n.121-5919A>G		intron	N/A
	ENSG00000307967	ENST00000830115.1		n.225-5919A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123827 AN: 152074 Hom.: 50680 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.814 AC: 123904 AN: 152192 Hom.: 50703 Cov.: 32 AF XY: 0.808 AC XY: 60106 AN XY: 74400

African (AFR) AF: 0.796 AC: 33057 AN: 41514

American (AMR) AF: 0.865 AC: 13227 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3088 AN: 3468

East Asian (EAS) AF: 0.755 AC: 3907 AN: 5172

South Asian (SAS) AF: 0.548 AC: 2639 AN: 4816

European-Finnish (FIN) AF: 0.787 AC: 8336 AN: 10588

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56909 AN: 68018

Other (OTH) AF: 0.823 AC: 1738 AN: 2112

Alfa AF: 0.820 Hom.: 16878

Bravo AF: 0.824

Asia WGS AF: 0.660 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.40
PhyloP100		-0.062
PromoterAI		0.045	Neutral
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: rs588702; hg19: chr13-77522925;