NM_018473.4:c.82-5932C>T

Variant names:

• chr6-24691951-C-T
• rs1885211
• NM_018473.4:c.82-5932C>T

Variant summary

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

The NM_018473.4(ACOT13):​c.82-5932C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,094 control chromosomes in the GnomAD database, including 24,170 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 0.56 (24170 hom., cov: 33)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 10 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]

LOC124901278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.82-5932C>T		intron_variant	Intron 1 of 2	ENST00000230048.5	NP_060943.1
LOC124901278	XR_007059508.1	n.3223G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ACOT13	NM_001160094.2	c.12+4258C>T		intron_variant	Intron 2 of 3		NP_001153566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOT13	ENST00000230048.5	c.82-5932C>T		intron_variant	Intron 1 of 2	1	NM_018473.4	ENSP00000230048.3
ACOT13	ENST00000537591.5	c.12+4258C>T		intron_variant	Intron 2 of 3	1		ENSP00000445552.1
ACOT13	ENST00000476436.1	n.292+4258C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85150 AN: 151976 Hom.: 24152 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.560 AC: 85209 AN: 152094 Hom.: 24170 Cov.: 33 AF XY: 0.556 AC XY: 41314 AN XY: 74350

African (AFR) AF: 0.542 AC: 22482 AN: 41448

American (AMR) AF: 0.482 AC: 7364 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2002 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2059 AN: 5174

South Asian (SAS) AF: 0.527 AC: 2542 AN: 4822

European-Finnish (FIN) AF: 0.588 AC: 6215 AN: 10568

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40502 AN: 68006

Other (OTH) AF: 0.530 AC: 1119 AN: 2110

Alfa AF: 0.582 Hom.: 55094

Bravo AF: 0.554

Asia WGS AF: 0.488 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.19
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: rs1885211; hg19: chr6-24692179;