chr6-24684793-A-G

Position:

• chr6-24684793-A-G

Variant summary

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

The NM_018473.4(ACOT13):​c.82-13090A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 151,966 control chromosomes in the GnomAD database, including 45,472 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 0.77 (45472 hom., cov: 30)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

Genes affected

ACOT13 (HGNC:20999): (acyl-CoA thioesterase 13) This gene encodes a member of the thioesterase superfamily. In humans, the protein co-localizes with microtubules and is essential for sustained cell proliferation. The orthologous mouse protein forms a homotetramer and is associated with mitochondria. The mouse protein functions as a medium- and long-chain acyl-CoA thioesterase. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.82-13090A>G		intron_variant		ENST00000230048.5	NP_060943.1
ACOT13	NM_001160094.2	c.-277-2612A>G		intron_variant			NP_001153566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOT13	ENST00000230048.5	c.82-13090A>G		intron_variant		1	NM_018473.4	ENSP00000230048	P1
ACOT13	ENST00000537591.5	c.-277-2612A>G		intron_variant		1		ENSP00000445552

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116462 AN: 151848 Hom.: 45411 Cov.: 30

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.767 AC: 116583 AN: 151966 Hom.: 45472 Cov.: 30 AF XY: 0.763 AC XY: 56638 AN XY: 74248

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.742

Alfa AF: 0.732 Hom.: 5108

Bravo AF: 0.789

Asia WGS AF: 0.793 AC: 2758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.70

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: rs1555086; hg19: chr6-24685021;