chr6-24673392-G-A

Position:

• chr6-24673392-G-A

Variant summary

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

The ENST00000230048.5(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 ENST00000230048.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.81+6048G>A		intron_variant		ENST00000230048.5	NP_060943.1
LOC124901279	XR_007059509.1	n.9884C>T		non_coding_transcript_exon_variant	1/2
ACOT13	NM_001160094.2	c.-278+6048G>A		intron_variant			NP_001153566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOT13	ENST00000230048.5	c.81+6048G>A		intron_variant		1	NM_018473.4	ENSP00000230048	P1
ACOT13	ENST00000537591.5	c.-278+6048G>A		intron_variant		1		ENSP00000445552

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

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.164

Alfa AF: 0.0279 Hom.: 36

Bravo AF: 0.193

Asia WGS AF: 0.308 AC: 1070 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.44

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: rs7765052; hg19: chr6-24673620;