NM_130767.3:c.497-4946C>T

Variant names:

• chr5-81352876-G-A
• rs7729671
• NM_130767.3:c.497-4946C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACOT12	NM_130767.3	c.497-4946C>T		intron_variant	Intron 5 of 14	ENST00000307624.8	NP_570123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOT12	ENST00000307624.8	c.497-4946C>T		intron_variant	Intron 5 of 14	1	NM_130767.3	ENSP00000303246.3

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

African (AFR) AF: 0.646 AC: 26767 AN: 41452

American (AMR) AF: 0.459 AC: 7009 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3464

East Asian (EAS) AF: 0.137 AC: 708 AN: 5180

South Asian (SAS) AF: 0.308 AC: 1485 AN: 4822

European-Finnish (FIN) AF: 0.352 AC: 3709 AN: 10542

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29555 AN: 67922

Other (OTH) AF: 0.473 AC: 999 AN: 2112

Alfa AF: 0.451 Hom.: 26604

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
PhyloP100		-1.2
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: rs7729671; hg19: chr5-80648695;