rs3181227

chr6-24667571-G-A

Variant summary

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

The NM_018473.4(ACOT13):c.81+227G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,150 control chromosomes in the GnomAD database, including 2,894 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 0.18 (2894 hom., cov: 32)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOT13	NM_018473.4	c.81+227G>A		intron_variant		ENST00000230048.5
ACOT13	NM_001160094.2	c.-278+227G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOT13	ENST00000230048.5	c.81+227G>A		intron_variant		1	NM_018473.4	P1
ACOT13	ENST00000537591.5	c.-278+227G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27748 AN: 152032 Hom.: 2893 Cov.: 32

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.182 AC: 27747 AN: 152150 Hom.: 2894 Cov.: 32 AF XY: 0.180 AC XY: 13373 AN XY: 74382

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.153

Alfa AF: 0.224 Hom.: 6811

Bravo AF: 0.176

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.48
Dann	Benign	0.73

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: rs3181227; hg19: chr6-24667799;