NM_018473.4:c.267-1452A>G

Variant names:

• chr6-24700007-A-G
• rs3777663
• NM_018473.4:c.267-1452A>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.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
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	NM_018473.4	MANE Select	c.267-1452A>G		intron	N/A	NP_060943.1
	ACOT13	NM_001160094.2		c.198-1452A>G		intron	N/A	NP_001153566.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	ENST00000230048.5	TSL:1 MANE Select	c.267-1452A>G		intron	N/A	ENSP00000230048.3
	ACOT13	ENST00000537591.5	TSL:1	c.198-1452A>G		intron	N/A	ENSP00000445552.1
	ACOT13	ENST00000476436.1	TSL:3	n.478-1452A>G		intron	N/A

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

African (AFR) AF: 0.0459 AC: 1907 AN: 41576

American (AMR) AF: 0.169 AC: 2593 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3472

East Asian (EAS) AF: 0.125 AC: 646 AN: 5184

South Asian (SAS) AF: 0.131 AC: 634 AN: 4830

European-Finnish (FIN) AF: 0.231 AC: 2446 AN: 10594

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16198 AN: 67990

Other (OTH) AF: 0.151 AC: 317 AN: 2106

Alfa AF: 0.215 Hom.: 6651

Bravo AF: 0.161

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		-0.13
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: rs3777663; hg19: chr6-24700235;