Variant chr1-6264687-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The ENST00000361521.9(ACOT7):c.1023C>T(p.Thr341=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,613,148 control chromosomes in the GnomAD database, including 234 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.023 ( 92 hom., cov: 33)

Exomes 𝑓: 0.0091 ( 142 hom. )

Consequence

ACOT7
ENST00000361521.9 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.94

Variant links:

Genes affected

ACOT7 (HGNC:24157): (acyl-CoA thioesterase 7) This gene encodes a member of the acyl coenzyme family. The encoded protein hydrolyzes the CoA thioester of palmitoyl-CoA and other long-chain fatty acids. Decreased expression of this gene may be associated with mesial temporal lobe epilepsy. Alternatively spliced transcript variants encoding distinct isoforms with different subcellular locations have been characterized. [provided by RefSeq, Jul 2008]

ACOT7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 1-6264687-G-A is Benign according to our data. Variant chr1-6264687-G-A is described in ClinVar as [Benign]. Clinvar id is 3055694.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.94 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOT7	NM_007274.4 linkuse as main transcript	c.1023C>T	p.Thr341=	synonymous_variant	9/9	ENST00000361521.9	NP_009205.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOT7	ENST00000361521.9 linkuse as main transcript	c.1023C>T	p.Thr341=	synonymous_variant	9/9	1	NM_007274.4	ENSP00000354615		O00154-7

Frequencies

GnomAD3 genomes

AF:

0.0231

AC:

3513

AN:

152218

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0608

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0162

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00435

Gnomad FIN

AF:

0.00932

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00739

Gnomad OTH

AF:

0.0291

GnomAD3 exomes

AF:

0.0115

AC:

2865

AN:

249556

Hom.:

AF XY:

0.0103

AC XY:

1390

AN XY:

135362

show subpopulations

Gnomad AFR exome

AF:

0.0603

Gnomad AMR exome

AF:

0.0128

Gnomad ASJ exome

AF:

0.0122

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00471

Gnomad FIN exome

AF:

0.00997

Gnomad NFE exome

AF:

0.00767

Gnomad OTH exome

AF:

0.0177

GnomAD4 exome

AF:

0.00911

AC:

13309

AN:

1460812

Hom.:

142

Cov.:

AF XY:

0.00885

AC XY:

6433

AN XY:

726736

show subpopulations

Gnomad4 AFR exome

AF:

0.0612

Gnomad4 AMR exome

AF:

0.0132

Gnomad4 ASJ exome

AF:

0.0121

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00488

Gnomad4 FIN exome

AF:

0.0100

Gnomad4 NFE exome

AF:

0.00751

Gnomad4 OTH exome

AF:

0.0138

GnomAD4 genome

AF:

0.0231

AC:

3514

AN:

152336

Hom.:

Cov.:

AF XY:

0.0231

AC XY:

1721

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.0606

Gnomad4 AMR

AF:

0.0162

Gnomad4 ASJ

AF:

0.0150

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00436

Gnomad4 FIN

AF:

0.00932

Gnomad4 NFE

AF:

0.00741

Gnomad4 OTH

AF:

0.0288

Alfa

AF:

0.0133

Hom.:

Bravo

AF:

0.0257

Asia WGS

AF:

0.00520

AC:

AN:

3478

EpiCase

AF:

0.0105

EpiControl

AF:

0.0101

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ACOT7-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 12, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

2.7

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over