Variant 5-41870266-T-TC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001364300.2(OXCT1):c.-524dupG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.011 in 1,608,674 control chromosomes in the GnomAD database, including 853 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 100 hom., cov: 32)

Exomes 𝑓: 0.011 ( 753 hom. )

Consequence

OXCT1
NM_001364300.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts U:1B:3

Conservation

PhyloP100: -0.667

Variant links:

Genes affected

OXCT1 (HGNC:8527): (3-oxoacid CoA-transferase 1) This gene encodes a member of the 3-oxoacid CoA-transferase gene family. The encoded protein is a homodimeric mitochondrial matrix enzyme that plays a central role in extrahepatic ketone body catabolism by catalyzing the reversible transfer of coenzyme A from succinyl-CoA to acetoacetate. Mutations in this gene are associated with succinyl CoA:3-oxoacid CoA transferase deficiency. [provided by RefSeq, Jul 2008]

OXCT1 links:

OXCT1-AS1 (HGNC:):

OXCT1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 5-41870266-T-TC is Benign according to our data. Variant chr5-41870266-T-TC is described in ClinVar as [Likely_benign]. Clinvar id is 93008.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXCT1	NM_000436.4 linkuse as main transcript	c.78+14dupG		intron_variant		ENST00000196371.10	NP_000427.1	P55809-1A0A024R040

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXCT1	ENST00000196371.10 linkuse as main transcript	c.78+14dupG		intron_variant		1	NM_000436.4	ENSP00000196371.5		P55809-1

Frequencies

GnomAD3 genomes

AF:

0.0141

AC:

2140

AN:

152016

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00280

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0753

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0313

Gnomad SAS

AF:

0.0774

Gnomad FIN

AF:

0.0224

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00103

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.0313

AC:

7843

AN:

250232

Hom.:

455

AF XY:

0.0296

AC XY:

4008

AN XY:

135414

show subpopulations

Gnomad AFR exome

AF:

0.00236

Gnomad AMR exome

AF:

0.131

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.0236

Gnomad SAS exome

AF:

0.0713

Gnomad FIN exome

AF:

0.0205

Gnomad NFE exome

AF:

0.00101

Gnomad OTH exome

AF:

0.0198

GnomAD4 exome

AF:

0.0107

AC:

15539

AN:

1456540

Hom.:

753

Cov.:

AF XY:

0.0120

AC XY:

8729

AN XY:

725076

show subpopulations

Gnomad4 AFR exome

AF:

0.00165

Gnomad4 AMR exome

AF:

0.122

Gnomad4 ASJ exome

AF:

0.000460

Gnomad4 EAS exome

AF:

0.0368

Gnomad4 SAS exome

AF:

0.0716

Gnomad4 FIN exome

AF:

0.0205

Gnomad4 NFE exome

AF:

0.000447

Gnomad4 OTH exome

AF:

0.0126

GnomAD4 genome

AF:

0.0142

AC:

2160

AN:

152134

Hom.:

100

Cov.:

AF XY:

0.0175

AC XY:

1298

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.00279

Gnomad4 AMR

AF:

0.0759

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.0314

Gnomad4 SAS

AF:

0.0783

Gnomad4 FIN

AF:

0.0224

Gnomad4 NFE

AF:

0.00103

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.00558

Hom.:

Bravo

AF:

0.0168

Asia WGS

AF:

0.0500

AC:

174

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Uncertain:1Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:1Benign:1

Uncertain significance, no assertion criteria provided	clinical testing	Eurofins Ntd Llc (ga)	Oct 02, 2012	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 20, 2021	- -

Succinyl-CoA acetoacetate transferase deficiency

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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