rs16889633

chr6-24703214-A-G

Variant summary

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

The NM_018473.4(ACOT13):c.*1599A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,282 control chromosomes in the GnomAD database, including 328 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 0.038 (328 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ACOT13 NM_018473.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

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 = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOT13	NM_018473.4	c.*1599A>G		3_prime_UTR_variant	3/3	ENST00000230048.5
ACOT13	NM_001160094.2	c.*1599A>G		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOT13	ENST00000230048.5	c.*1599A>G		3_prime_UTR_variant	3/3	1	NM_018473.4	P1
ACOT13	ENST00000537591.5	c.*1599A>G		3_prime_UTR_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.0375 AC: 5713 AN: 152164 Hom.: 321 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00585

Gnomad OTH AF: 0.0397

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0378 AC: 5751 AN: 152282 Hom.: 328 Cov.: 32 AF XY: 0.0363 AC XY: 2703 AN XY: 74460

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.00207

Gnomad4 FIN AF: 0.00226

Gnomad4 NFE AF: 0.00585

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0162 Hom.: 32

Bravo AF: 0.0439

Asia WGS AF: 0.0120 AC: 41 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	12
Dann	Benign	0.73

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: rs16889633; hg19: chr6-24703442;