6-24697196-T-C

Position:

• chr6-24697196-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.82-687T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,252 control chromosomes in the GnomAD database, including 7,288 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 0.30 (7288 hom., cov: 33)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.82-687T>C		intron_variant		ENST00000230048.5	NP_060943.1
ACOT13	NM_001160094.2	c.13-687T>C		intron_variant			NP_001153566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOT13	ENST00000230048.5	c.82-687T>C		intron_variant		1	NM_018473.4	ENSP00000230048	P1
ACOT13	ENST00000537591.5	c.13-687T>C		intron_variant		1		ENSP00000445552
ACOT13	ENST00000476436.1	n.293-687T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45875 AN: 152134 Hom.: 7290 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.284

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.301 AC: 45872 AN: 152252 Hom.: 7288 Cov.: 33 AF XY: 0.298 AC XY: 22165 AN XY: 74432

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.281

Alfa AF: 0.336 Hom.: 2970

Bravo AF: 0.295

Asia WGS AF: 0.281 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.66

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: rs6904345; hg19: chr6-24697424;