Variant rs1702003 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_147161.4(ACOT11):c.605G>A(p.Gly202Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 1,609,904 control chromosomes in the GnomAD database, including 13,105 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. 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 0.17 ( 4857 hom., cov: 33)

Exomes 𝑓: 0.059 ( 8248 hom. )

Consequence

ACOT11
NM_147161.4 missense, splice_region

Scores

Splicing: ADA: 0.000006643

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.73

Variant links:

Genes affected

ACOT11 (HGNC:18156): (acyl-CoA thioesterase 11) This gene encodes a member of the acyl-CoA thioesterase family which catalyse the conversion of activated fatty acids to the corresponding non-esterified fatty acid and coenzyme A. Expression of a mouse homolog in brown adipose tissue is induced by low temperatures and repressed by warm temperatures. Higher levels of expression of the mouse homolog has been found in obesity-resistant mice compared with obesity-prone mice, suggesting a role of acyl-CoA thioesterase 11 in obesity. Alternative splicing results in transcript variants. [provided by RefSeq, Nov 2010]

ACOT11 links:

ACOT11 (HGNC:):

ACOT11 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=0.0012792647).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOT11	NM_147161.4 linkuse as main transcript	c.605G>A	p.Gly202Asp	missense_variant, splice_region_variant	6/16	ENST00000343744.7	NP_671517.1	Q8WXI4-2
ACOT11	NM_015547.4 linkuse as main transcript	c.605G>A	p.Gly202Asp	missense_variant, splice_region_variant	6/17		NP_056362.1	Q8WXI4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ACOT11	ENST00000343744.7 linkuse as main transcript	c.605G>A	p.Gly202Asp	missense_variant, splice_region_variant	6/16	1	NM_147161.4	ENSP00000340260.2	Q8WXI4-2
ACOT11	ENST00000371316.3 linkuse as main transcript	c.605G>A	p.Gly202Asp	missense_variant, splice_region_variant	6/17	1		ENSP00000360366.3	Q8WXI4-1
ACOT11	ENST00000481208.5 linkuse as main transcript	n.683G>A		splice_region_variant, non_coding_transcript_exon_variant	5/15	2
ACOT11	ENST00000498228.1 linkuse as main transcript	n.848G>A		splice_region_variant, non_coding_transcript_exon_variant	7/8	2

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25806

AN:

152158

Hom.:

4838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.461

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.0400

Gnomad EAS

AF:

0.195

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.0375

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0302

Gnomad OTH

AF:

0.131

GnomAD3 exomes

AF:

0.112

AC:

27741

AN:

246820

Hom.:

3421

AF XY:

0.107

AC XY:

14231

AN XY:

133522

show subpopulations

Gnomad AFR exome

AF:

0.466

Gnomad AMR exome

AF:

0.154

Gnomad ASJ exome

AF:

0.0510

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.205

Gnomad FIN exome

AF:

0.0364

Gnomad NFE exome

AF:

0.0298

Gnomad OTH exome

AF:

0.0849

GnomAD4 exome

AF:

0.0590

AC:

86040

AN:

1457628

Hom.:

8248

Cov.:

AF XY:

0.0620

AC XY:

44940

AN XY:

724486

show subpopulations

Gnomad4 AFR exome

AF:

0.474

Gnomad4 AMR exome

AF:

0.148

Gnomad4 ASJ exome

AF:

0.0493

Gnomad4 EAS exome

AF:

0.216

Gnomad4 SAS exome

AF:

0.207

Gnomad4 FIN exome

AF:

0.0369

Gnomad4 NFE exome

AF:

0.0257

Gnomad4 OTH exome

AF:

0.0847

GnomAD4 genome

AF:

0.170

AC:

25873

AN:

152276

Hom.:

4857

Cov.:

AF XY:

0.169

AC XY:

12608

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.0400

Gnomad4 EAS

AF:

0.194

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.0375

Gnomad4 NFE

AF:

0.0302

Gnomad4 OTH

AF:

0.131

Alfa

AF:

0.0692

Hom.:

1850

Bravo

AF:

0.187

TwinsUK

AF:

0.0262

AC:

ALSPAC

AF:

0.0265

AC:

102

ESP6500AA

AF:

0.448

AC:

1976

ESP6500EA

AF:

0.0297

AC:

255

ExAC

AF:

0.117

AC:

14222

Asia WGS

AF:

0.226

AC:

785

AN:

3478

EpiCase

AF:

0.0285

EpiControl

AF:

0.0333

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.19

DEOGEN2

Benign

0.0048

.;T

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.76

FATHMM_MKL

Benign

0.031

LIST_S2

Benign

0.12

T;T

MetaRNN

Benign

0.0013

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-1.7

N;N

PrimateAI

Uncertain

0.49

PROVEAN

Benign

0.78

N;N

REVEL

Benign

0.040

Sift

Benign

1.0

T;T

Sift4G

Benign

0.81

T;T

Polyphen

0.0

B;B

Vest4

0.079

MPC

0.25

ClinPred

0.0012

GERP RS

3.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.038

gMVP

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0000066

dbscSNV1_RF

Benign

0.0

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