rs2143338

Variant names:

• chr6-24683053-T-C
• rs2143338
• NM_018473.4:c.82-14830T>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.82-14830T>C 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 152,182 control chromosomes in the GnomAD database, including 2,887 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 (2887 hom., cov: 31)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 1 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]

LOC124901279 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• 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 rank	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.82-14830T>C		intron_variant	Intron 1 of 2	ENST00000230048.5	NP_060943.1
LOC124901279	XR_007059509.1	n.223A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ACOT13	NM_001160094.2	c.-277-4352T>C		intron_variant	Intron 1 of 3		NP_001153566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOT13	ENST00000230048.5	c.82-14830T>C		intron_variant	Intron 1 of 2	1	NM_018473.4	ENSP00000230048.3
ACOT13	ENST00000537591.5	c.-277-4352T>C		intron_variant	Intron 1 of 3	1		ENSP00000445552.1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27741 AN: 152064 Hom.: 2886 Cov.: 31

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.229

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: 27740 AN: 152182 Hom.: 2887 Cov.: 31 AF XY: 0.180 AC XY: 13363 AN XY: 74394

African (AFR) AF: 0.0841 AC: 3494 AN: 41526

American (AMR) AF: 0.177 AC: 2700 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3470

East Asian (EAS) AF: 0.151 AC: 780 AN: 5178

South Asian (SAS) AF: 0.133 AC: 642 AN: 4830

European-Finnish (FIN) AF: 0.229 AC: 2424 AN: 10582

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16266 AN: 67994

Other (OTH) AF: 0.153 AC: 322 AN: 2110

Alfa AF: 0.199 Hom.: 427

Bravo AF: 0.176

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.8
DANN	Benign	0.91
PhyloP100		0.15
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: rs2143338; hg19: chr6-24683281;