rs3777663

chr6-24700007-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.267-1452A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,252 control chromosomes in the GnomAD database, including 2,697 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 0.17 (2697 hom., cov: 32)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOT13	NM_018473.4	c.267-1452A>G		intron_variant		ENST00000230048.5
ACOT13	NM_001160094.2	c.198-1452A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOT13	ENST00000230048.5	c.267-1452A>G		intron_variant		1	NM_018473.4	P1
ACOT13	ENST00000537591.5	c.198-1452A>G		intron_variant		1
ACOT13	ENST00000476436.1	n.478-1452A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25793 AN: 152134 Hom.: 2698 Cov.: 32

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.169 AC: 25785 AN: 152252 Hom.: 2697 Cov.: 32 AF XY: 0.167 AC XY: 12429 AN XY: 74450

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.151

Alfa AF: 0.218 Hom.: 4984

Bravo AF: 0.161

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.51

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: rs3777663; hg19: chr6-24700235;