rs7729671

chr5-81352876-G-A

Variant summary

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

The NM_130767.3(ACOT12):c.497-4946C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,974 control chromosomes in the GnomAD database, including 18,291 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 0.48 (18291 hom., cov: 32)
• Consequence: ACOT12 NM_130767.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOT12	NM_130767.3	c.497-4946C>T		intron_variant		ENST00000307624.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOT12	ENST00000307624.8	c.497-4946C>T		intron_variant		1	NM_130767.3	P1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72170 AN: 151856 Hom.: 18247 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.475 AC: 72250 AN: 151974 Hom.: 18291 Cov.: 32 AF XY: 0.467 AC XY: 34706 AN XY: 74278

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.473

Alfa AF: 0.444 Hom.: 20307

Bravo AF: 0.496

Asia WGS AF: 0.263 AC: 915 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	0.69
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: rs7729671; hg19: chr5-80648695;