6-24688730-A-G

Variant names:

• chr6-24688730-A-G
• rs1885209
• NM_018473.4:c.82-9153A>G

Variant summary

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

The NM_018473.4(ACOT13):​c.82-9153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,092 control chromosomes in the GnomAD database, including 45,416 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 (45416 hom., cov: 31)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 1 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018473.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	NM_018473.4	MANE Select	c.82-9153A>G		intron	N/A	NP_060943.1	Q9NPJ3-1
	ACOT13	NM_001160094.2		c.12+1037A>G		intron	N/A	NP_001153566.1	Q9NPJ3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	ENST00000230048.5	TSL:1 MANE Select	c.82-9153A>G		intron	N/A	ENSP00000230048.3	Q9NPJ3-1
	ACOT13	ENST00000537591.5	TSL:1	c.12+1037A>G		intron	N/A	ENSP00000445552.1	Q9NPJ3-2
	ACOT13	ENST00000858847.1		c.82-9153A>G		intron	N/A	ENSP00000528906.1

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116458 AN: 151974 Hom.: 45356 Cov.: 31

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.798

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: 0.766 AC: 116578 AN: 152092 Hom.: 45416 Cov.: 31 AF XY: 0.762 AC XY: 56647 AN XY: 74314

African (AFR) AF: 0.904 AC: 37533 AN: 41518

American (AMR) AF: 0.798 AC: 12201 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2430 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4414 AN: 5168

South Asian (SAS) AF: 0.724 AC: 3495 AN: 4826

European-Finnish (FIN) AF: 0.630 AC: 6635 AN: 10524

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47267 AN: 67986

Other (OTH) AF: 0.743 AC: 1564 AN: 2106

Alfa AF: 0.803 Hom.: 10652

Bravo AF: 0.788

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.49
PhyloP100		-0.37
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: rs1885209; hg19: chr6-24688958; COSMIC: COSV57764925;