5-81359147-T-G

Position:

• chr5-81359147-T-G

Variant summary

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

The NM_130767.3(ACOT12):​c.496+756A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,144 control chromosomes in the GnomAD database, including 61,326 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 0.89 (61326 hom., cov: 31)
• Consequence: ACOT12 NM_130767.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

Genes affected

ACOT12 (HGNC:24436): (acyl-CoA thioesterase 12) Enables identical protein binding activity. Predicted to be involved in acyl-CoA metabolic process and fatty acid metabolic process. Predicted to act upstream of or within acetyl-CoA metabolic process. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

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 (AFR) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOT12	NM_130767.3	c.496+756A>C		intron_variant		ENST00000307624.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOT12	ENST00000307624.8	c.496+756A>C		intron_variant		1	NM_130767.3	P1

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135760 AN: 152026 Hom.: 61273 Cov.: 31

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.893 AC: 135863 AN: 152144 Hom.: 61326 Cov.: 31 AF XY: 0.887 AC XY: 65974 AN XY: 74380

Gnomad4 AFR AF: 0.976

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.883

Alfa AF: 0.894 Hom.: 79551

Bravo AF: 0.891

Asia WGS AF: 0.701 AC: 2439 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	0.70
DANN	Benign	0.74

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: rs4703516; hg19: chr5-80654966;