rs17243157

Positions:

• chr6-24667095-C-T

Variant summary

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

The NM_018473.4(ACOT13):​c.-169C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 847,006 control chromosomes in the GnomAD database, including 6,313 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 0.10 (884 hom., cov: 34)
  • Exomes 𝑓: 0.12 (5429 hom.)
• Consequence: ACOT13 NM_018473.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) 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.-169C>T		5_prime_UTR_variant	1/3	ENST00000230048.5
ACOT13	NM_001160094.2	c.-527C>T		5_prime_UTR_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOT13	ENST00000230048.5	c.-169C>T		5_prime_UTR_variant	1/3	1	NM_018473.4	P1
ACOT13	ENST00000537591.5	c.-527C>T		5_prime_UTR_variant	1/4	1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15246 AN: 152066 Hom.: 885 Cov.: 34

Gnomad AFR AF: 0.0634

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.0910

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.117 AC: 81617 AN: 694820 Hom.: 5429 Cov.: 9 AF XY: 0.123 AC XY: 43820 AN XY: 356554

Gnomad4 AFR exome AF: 0.0596

Gnomad4 AMR exome AF: 0.0834

Gnomad4 ASJ exome AF: 0.128

Gnomad4 EAS exome AF: 0.102

Gnomad4 SAS exome AF: 0.236

Gnomad4 FIN exome AF: 0.0928

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.120

GnomAD4 genome AF: 0.100 AC: 15236 AN: 152186 Hom.: 884 Cov.: 34 AF XY: 0.100 AC XY: 7464 AN XY: 74412

Gnomad4 AFR AF: 0.0633

Gnomad4 AMR AF: 0.0909

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0911

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.105

Alfa AF: 0.113 Hom.: 1084

Bravo AF: 0.0959

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.7
DANN	Benign	0.77
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs17243157; hg19: chr6-24667323; COSMIC: COSV57765608; COSMIC: COSV57765608;