NM_018473.4:c.81+12356A>G

Variant names:

• chr6-24679700-A-G
• rs2328847
• NM_018473.4:c.81+12356A>G

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+12356A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,202 control chromosomes in the GnomAD database, including 2,241 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 0.11 (2241 hom., cov: 32)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 1 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=-0.84).
• 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+12356A>G		intron	N/A	NP_060943.1
	ACOT13	NM_001160094.2		c.-277-7705A>G		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+12356A>G		intron	N/A	ENSP00000230048.3
	ACOT13	ENST00000537591.5	TSL:1	c.-277-7705A>G		intron	N/A	ENSP00000445552.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17178 AN: 152084 Hom.: 2236 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.00924

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.113 AC: 17215 AN: 152202 Hom.: 2241 Cov.: 32 AF XY: 0.119 AC XY: 8826 AN XY: 74438

African (AFR) AF: 0.212 AC: 8811 AN: 41502

American (AMR) AF: 0.251 AC: 3829 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3472

East Asian (EAS) AF: 0.485 AC: 2511 AN: 5174

South Asian (SAS) AF: 0.153 AC: 737 AN: 4824

European-Finnish (FIN) AF: 0.00924 AC: 98 AN: 10608

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0121 AC: 824 AN: 68022

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.0634 Hom.: 116

Bravo AF: 0.137

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.8
DANN	Benign	0.88
PhyloP100		0.15
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: rs2328847; hg19: chr6-24679928;