6-24673392-G-A

Variant names:

• chr6-24673392-G-A
• rs7765052
• NM_018473.4:c.81+6048G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018473.4(ACOT13):​c.81+6048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,668 control chromosomes in the GnomAD database, including 3,732 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 0.16 (3732 hom., cov: 32)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018473.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	NM_018473.4	MANE Select	c.81+6048G>A		intron	N/A	NP_060943.1
	ACOT13	NM_001160094.2		c.-278+6048G>A		intron	N/A	NP_001153566.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOT13	ENST00000230048.5	TSL:1 MANE Select	c.81+6048G>A		intron	N/A	ENSP00000230048.3
	ACOT13	ENST00000537591.5	TSL:1	c.-278+6048G>A		intron	N/A	ENSP00000445552.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24748 AN: 151550 Hom.: 3716 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.164 AC: 24804 AN: 151668 Hom.: 3732 Cov.: 32 AF XY: 0.167 AC XY: 12350 AN XY: 74110

African (AFR) AF: 0.325 AC: 13436 AN: 41308

American (AMR) AF: 0.286 AC: 4368 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2506 AN: 5166

South Asian (SAS) AF: 0.152 AC: 728 AN: 4790

European-Finnish (FIN) AF: 0.0161 AC: 168 AN: 10422

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0439 AC: 2980 AN: 67938

Other (OTH) AF: 0.164 AC: 346 AN: 2106

Alfa AF: 0.0406 Hom.: 76

Bravo AF: 0.193

Asia WGS AF: 0.308 AC: 1070 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7765052; hg19: chr6-24673620;