rs1053598

chr6-24704310-T-C

Variant summary

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

The NM_018473.4(ACOT13):c.*2695T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,148 control chromosomes in the GnomAD database, including 37,257 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 0.69 (37257 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ACOT13 NM_018473.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOT13	NM_018473.4	c.*2695T>C		3_prime_UTR_variant	3/3	ENST00000230048.5
ACOT13	NM_001160094.2	c.*2695T>C		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOT13	ENST00000230048.5	c.*2695T>C		3_prime_UTR_variant	3/3	1	NM_018473.4	P1
ACOT13	ENST00000537591.5	c.*2695T>C		3_prime_UTR_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105435 AN: 152030 Hom.: 37211 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.671

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.694 AC: 105531 AN: 152148 Hom.: 37257 Cov.: 33 AF XY: 0.684 AC XY: 50855 AN XY: 74388

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.673

Alfa AF: 0.702 Hom.: 53480

Bravo AF: 0.693

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.55
Dann	Benign	0.83

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: rs1053598; hg19: chr6-24704538;