6-24687537-A-G

Variant names:

• chr6-24687537-A-G
• rs926529
• ENST00000537591.5:c.-145A>G

Variant summary

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

The ENST00000537591.5(ACOT13):​c.-145A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 1,391,454 control chromosomes in the GnomAD database, including 353,681 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 (45258 hom., cov: 29)
  • Exomes 𝑓: 0.70 (308423 hom.)
• Consequence: ACOT13 ENST00000537591.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 10 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537591.5. 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
	ACOT13	NM_018473.4	MANE Select	c.82-10346A>G		intron	N/A	NP_060943.1
	ACOT13	NM_001160094.2		c.-145A>G		5_prime_UTR	Exon 2 of 4	NP_001153566.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	ENST00000537591.5	TSL:1	c.-145A>G		5_prime_UTR	Exon 2 of 4	ENSP00000445552.1
	ACOT13	ENST00000230048.5	TSL:1 MANE Select	c.82-10346A>G		intron	N/A	ENSP00000230048.3
	ACOT13	ENST00000476436.1	TSL:3	n.136A>G		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116192 AN: 151798 Hom.: 45199 Cov.: 29

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.821

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.739

GnomAD4 exome AF: 0.703 AC: 871550 AN: 1239538 Hom.: 308423 Cov.: 37 AF XY: 0.702 AC XY: 421067 AN XY: 599582

African (AFR) AF: 0.912 AC: 23683 AN: 25974

American (AMR) AF: 0.806 AC: 12247 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 12311 AN: 17524

East Asian (EAS) AF: 0.875 AC: 27664 AN: 31610

South Asian (SAS) AF: 0.708 AC: 35922 AN: 50724

European-Finnish (FIN) AF: 0.631 AC: 27012 AN: 42782

Middle Eastern (MID) AF: 0.775 AC: 3898 AN: 5032

European-Non Finnish (NFE) AF: 0.692 AC: 692090 AN: 1000010

Other (OTH) AF: 0.724 AC: 36723 AN: 50696

GnomAD4 genome AF: 0.766 AC: 116311 AN: 151916 Hom.: 45258 Cov.: 29 AF XY: 0.761 AC XY: 56492 AN XY: 74212

African (AFR) AF: 0.903 AC: 37383 AN: 41408

American (AMR) AF: 0.798 AC: 12196 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2428 AN: 3466

East Asian (EAS) AF: 0.853 AC: 4401 AN: 5158

South Asian (SAS) AF: 0.710 AC: 3420 AN: 4814

European-Finnish (FIN) AF: 0.630 AC: 6621 AN: 10516

Middle Eastern (MID) AF: 0.817 AC: 237 AN: 290

European-Non Finnish (NFE) AF: 0.695 AC: 47255 AN: 67958

Other (OTH) AF: 0.742 AC: 1568 AN: 2112

Alfa AF: 0.699 Hom.: 16621

Bravo AF: 0.788

Asia WGS AF: 0.790 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.76
PhyloP100		1.2
Mutation Taster		=299/1	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: rs926529; hg19: chr6-24687765;