rs4544900

Positions:

• chr6-24677760-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.81+10416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,142 control chromosomes in the GnomAD database, including 3,229 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 (3229 hom., cov: 32)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

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]

LOC124901279 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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/exons	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.81+10416C>T		intron_variant		ENST00000230048.5	NP_060943.1
LOC124901279	XR_007059509.1	n.5516G>A		non_coding_transcript_exon_variant	1/2
ACOT13	NM_001160094.2	c.-277-9645C>T		intron_variant			NP_001153566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOT13	ENST00000230048.5	c.81+10416C>T		intron_variant		1	NM_018473.4	ENSP00000230048	P1
ACOT13	ENST00000537591.5	c.-277-9645C>T		intron_variant		1		ENSP00000445552

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28453 AN: 152024 Hom.: 3226 Cov.: 32

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.187 AC: 28471 AN: 152142 Hom.: 3229 Cov.: 32 AF XY: 0.187 AC XY: 13885 AN XY: 74396

Gnomad4 AFR AF: 0.0757

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.193

Alfa AF: 0.218 Hom.: 659

Bravo AF: 0.173

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.39

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: rs4544900; hg19: chr6-24677988;