Variant rs10371 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_130767.3(ACOT12):c.1207G>A(p.Ala403Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,612,838 control chromosomes in the GnomAD database, including 19,691 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.15 ( 1806 hom., cov: 33)

Exomes 𝑓: 0.15 ( 17885 hom. )

Consequence

ACOT12
NM_130767.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.33

Variant links:

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]

ACOT12 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015539527).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOT12	NM_130767.3 linkuse as main transcript	c.1207G>A	p.Ala403Thr	missense_variant	12/15	ENST00000307624.8	NP_570123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOT12	ENST00000307624.8 linkuse as main transcript	c.1207G>A	p.Ala403Thr	missense_variant	12/15	1	NM_130767.3	ENSP00000303246	P1	Q8WYK0-1
ACOT12	ENST00000506440.1 linkuse as main transcript	n.80G>A		non_coding_transcript_exon_variant	1/3	2
ACOT12	ENST00000508234.5 linkuse as main transcript	n.187G>A		non_coding_transcript_exon_variant	3/6	3

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23139

AN:

152006

Hom.:

1803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.00424

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.163

GnomAD3 exomes

AF:

0.131

AC:

32844

AN:

251092

Hom.:

2405

AF XY:

0.133

AC XY:

18012

AN XY:

135700

show subpopulations

Gnomad AFR exome

AF:

0.186

Gnomad AMR exome

AF:

0.0887

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.00169

Gnomad SAS exome

AF:

0.127

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.158

Gnomad OTH exome

AF:

0.151

GnomAD4 exome

AF:

0.153

AC:

223445

AN:

1460714

Hom.:

17885

Cov.:

AF XY:

0.152

AC XY:

110582

AN XY:

726622

show subpopulations

Gnomad4 AFR exome

AF:

0.187

Gnomad4 AMR exome

AF:

0.0918

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.00191

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.163

Gnomad4 OTH exome

AF:

0.154

GnomAD4 genome

AF:

0.152

AC:

23163

AN:

152124

Hom.:

1806

Cov.:

AF XY:

0.149

AC XY:

11109

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.00425

Gnomad4 SAS

AF:

0.117

Gnomad4 FIN

AF:

0.109

Gnomad4 NFE

AF:

0.158

Gnomad4 OTH

AF:

0.160

Alfa

AF:

0.159

Hom.:

2205

Bravo

AF:

0.155

TwinsUK

AF:

0.170

AC:

630

ALSPAC

AF:

0.164

AC:

631

ESP6500AA

AF:

0.193

AC:

849

ESP6500EA

AF:

0.156

AC:

1345

ExAC

AF:

0.136

AC:

16498

Asia WGS

AF:

0.0760

AC:

266

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.088

Eigen

Benign

-0.50

Eigen_PC

Benign

-0.43

FATHMM_MKL

Benign

0.52

LIST_S2

Benign

0.69

MetaRNN

Benign

0.0016

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.3

MutationTaster

Benign

0.99

PrimateAI

Benign

0.33

PROVEAN

Benign

-1.5

REVEL

Benign

0.028

Sift

Benign

0.17

Sift4G

Benign

0.24

Polyphen

0.051

Vest4

0.077

MPC

0.10

ClinPred

0.010

GERP RS

4.3

Varity_R

0.037

gMVP

0.28

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over