Variant 14-73537589-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000311148.9(ACOT1):c.168C>T(p.Thr56=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 69 hom., cov: 19)

Exomes 𝑓: 0.00048 ( 158 hom. )

Failed GnomAD Quality Control

Consequence

ACOT1
ENST00000311148.9 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.185

Variant links:

Genes affected

ACOT1 (HGNC:33128): (acyl-CoA thioesterase 1) Enables acyl-CoA hydrolase activity. Involved in acyl-CoA metabolic process; long-chain fatty acid metabolic process; and very long-chain fatty acid metabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACOT1 links:

HEATR4 (HGNC:16761): (HEAT repeat containing 4) Predicted to enable oxidoreductase activity. [provided by Alliance of Genome Resources, Apr 2022]

HEATR4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 14-73537589-C-T is Benign according to our data. Variant chr14-73537589-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 778484.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.185 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 69 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOT1	NM_001037161.2 linkuse as main transcript	c.168C>T	p.Thr56=	synonymous_variant	1/3	ENST00000311148.9	NP_001032238.1
HEATR4	NM_001220484.1 linkuse as main transcript	c.-151-7345G>A		intron_variant		ENST00000553558.6	NP_001207413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOT1	ENST00000311148.9 linkuse as main transcript	c.168C>T	p.Thr56=	synonymous_variant	1/3	1	NM_001037161.2	ENSP00000311224	P1
HEATR4	ENST00000553558.6 linkuse as main transcript	c.-151-7345G>A		intron_variant		2	NM_001220484.1	ENSP00000450444	P1

Frequencies

GnomAD3 genomes

AF:

0.00366

AC:

425

AN:

116160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00798

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.00111

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00105

Gnomad FIN

AF:

0.00248

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00145

Gnomad OTH

AF:

0.00649

GnomAD3 exomes

AF:

0.00128

AC:

162

AN:

126710

Hom.:

AF XY:

0.00126

AC XY:

AN XY:

71612

show subpopulations

Gnomad AFR exome

AF:

0.00260

Gnomad AMR exome

AF:

0.000409

Gnomad ASJ exome

AF:

0.000330

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000540

Gnomad FIN exome

AF:

0.00181

Gnomad NFE exome

AF:

0.00174

Gnomad OTH exome

AF:

0.00152

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000482

AC:

527

AN:

1092414

Hom.:

158

Cov.:

AF XY:

0.000440

AC XY:

239

AN XY:

542676

show subpopulations

Gnomad4 AFR exome

AF:

0.00506

Gnomad4 AMR exome

AF:

0.000403

Gnomad4 ASJ exome

AF:

0.000420

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000136

Gnomad4 FIN exome

AF:

0.000490

Gnomad4 NFE exome

AF:

0.000345

Gnomad4 OTH exome

AF:

0.00110

GnomAD4 genome

AF:

0.00367

AC:

426

AN:

116220

Hom.:

Cov.:

AF XY:

0.00369

AC XY:

207

AN XY:

56052

show subpopulations

Gnomad4 AFR

AF:

0.00799

Gnomad4 AMR

AF:

0.00241

Gnomad4 ASJ

AF:

0.00111

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00106

Gnomad4 FIN

AF:

0.00248

Gnomad4 NFE

AF:

0.00145

Gnomad4 OTH

AF:

0.00640

Alfa

AF:

0.00379

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.92

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