NM_018473.4:c.82-687T>C

Variant names:

• chr6-24697196-T-C
• rs6904345
• NM_018473.4:c.82-687T>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.82-687T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,252 control chromosomes in the GnomAD database, including 7,288 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 0.30 (7288 hom., cov: 33)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	NM_018473.4	MANE Select	c.82-687T>C		intron	N/A	NP_060943.1	Q9NPJ3-1
	ACOT13	NM_001160094.2		c.13-687T>C		intron	N/A	NP_001153566.1	Q9NPJ3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	ENST00000230048.5	TSL:1 MANE Select	c.82-687T>C		intron	N/A	ENSP00000230048.3	Q9NPJ3-1
	ACOT13	ENST00000537591.5	TSL:1	c.13-687T>C		intron	N/A	ENSP00000445552.1	Q9NPJ3-2
	ACOT13	ENST00000858847.1		c.82-687T>C		intron	N/A	ENSP00000528906.1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45875 AN: 152134 Hom.: 7290 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.301 AC: 45872 AN: 152252 Hom.: 7288 Cov.: 33 AF XY: 0.298 AC XY: 22165 AN XY: 74432

African (AFR) AF: 0.216 AC: 8969 AN: 41542

American (AMR) AF: 0.275 AC: 4200 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1157 AN: 5188

South Asian (SAS) AF: 0.378 AC: 1828 AN: 4830

European-Finnish (FIN) AF: 0.316 AC: 3345 AN: 10594

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23944 AN: 68020

Other (OTH) AF: 0.281 AC: 593 AN: 2112

Alfa AF: 0.330 Hom.: 3140

Bravo AF: 0.295

Asia WGS AF: 0.281 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.66
PhyloP100		-0.79
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: rs6904345; hg19: chr6-24697424;