13-76948790-T-C

Position:

• chr13-76948790-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC105370269 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOD1	NM_001258406.2	c.12+220T>C		intron_variant		ENST00000377462.6
LOC105370269	XR_001749929.1	n.213-5919A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOD1	ENST00000377462.6	c.12+220T>C		intron_variant		5	NM_001258406.2	P1

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

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.823

Alfa AF: 0.829 Hom.: 8345

Bravo AF: 0.824

Asia WGS AF: 0.660 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.40

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: rs588702; hg19: chr13-77522925;