6-24697160-A-C

Variant names:

• chr6-24697160-A-C
• rs2092404
• NM_018473.4:c.82-723A>C

Variant summary

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

The NM_018473.4(ACOT13):​c.82-723A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,232 control chromosomes in the GnomAD database, including 43,087 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 0.75 (43087 hom., cov: 34)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.82-723A>C		intron_variant	Intron 1 of 2	ENST00000230048.5	NP_060943.1
ACOT13	NM_001160094.2	c.13-723A>C		intron_variant	Intron 2 of 3		NP_001153566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOT13	ENST00000230048.5	c.82-723A>C		intron_variant	Intron 1 of 2	1	NM_018473.4	ENSP00000230048.3
ACOT13	ENST00000537591.5	c.13-723A>C		intron_variant	Intron 2 of 3	1		ENSP00000445552.1
ACOT13	ENST00000476436.1	n.293-723A>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113954 AN: 152114 Hom.: 43042 Cov.: 34

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.749 AC: 114057 AN: 152232 Hom.: 43087 Cov.: 34 AF XY: 0.747 AC XY: 55629 AN XY: 74424

African (AFR) AF: 0.825 AC: 34287 AN: 41552

American (AMR) AF: 0.792 AC: 12113 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2408 AN: 3472

East Asian (EAS) AF: 0.850 AC: 4413 AN: 5190

South Asian (SAS) AF: 0.738 AC: 3566 AN: 4830

European-Finnish (FIN) AF: 0.666 AC: 7044 AN: 10576

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47687 AN: 67998

Other (OTH) AF: 0.725 AC: 1530 AN: 2110

Alfa AF: 0.715 Hom.: 17277

Bravo AF: 0.764

Asia WGS AF: 0.799 AC: 2777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.54
DANN	Benign	0.47
PhyloP100		-0.39
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: rs2092404; hg19: chr6-24697388;