6-24667434-C-T

Variant names:

• chr6-24667434-C-T
• rs3181228
• NM_018473.4:c.81+90C>T

Variant summary

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

The NM_018473.4(ACOT13):​c.81+90C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,178,496 control chromosomes in the GnomAD database, including 31,307 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 0.19 (3321 hom., cov: 32)
  • Exomes 𝑓: 0.22 (27986 hom.)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.81+90C>T		intron_variant	Intron 1 of 2	ENST00000230048.5	NP_060943.1
ACOT13	NM_001160094.2	c.-278+90C>T		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.81+90C>T		intron_variant	Intron 1 of 2	1	NM_018473.4	ENSP00000230048.3
ACOT13	ENST00000537591.5	c.-278+90C>T		intron_variant	Intron 1 of 3	1		ENSP00000445552.1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29599 AN: 152052 Hom.: 3317 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.222 AC: 227954 AN: 1026326 Hom.: 27986 AF XY: 0.222 AC XY: 116604 AN XY: 524330

Gnomad4 AFR exome AF: 0.0919

Gnomad4 AMR exome AF: 0.130

Gnomad4 ASJ exome AF: 0.223

Gnomad4 EAS exome AF: 0.0353

Gnomad4 SAS exome AF: 0.171

Gnomad4 FIN exome AF: 0.268

Gnomad4 NFE exome AF: 0.243

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.195 AC: 29619 AN: 152170 Hom.: 3321 Cov.: 32 AF XY: 0.194 AC XY: 14395 AN XY: 74388

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.197

Alfa AF: 0.233 Hom.: 4311

Bravo AF: 0.182

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.1
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3181228; hg19: chr6-24667662;