Genetic Variant OXCT1:c.78+14dupG (chr5-41870266-T-TC) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

0 publications found

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:40423): (OXCT1 antisense RNA 1)

OXCT1-AS1 links:

LOC102723752 (HGNC:):

LOC102723752 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 Benign/Likely_benign. ClinVar VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364300.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OXCT1	NM_000436.4	MANE Select	c.78+14dupG	intron	N/A	NP_000427.1	P55809-1
OXCT1	NM_001364300.2		c.-524dupG	5_prime_UTR	Exon 1 of 17	NP_001351229.1
OXCT1	NM_001364299.2		c.78+14dupG	intron	N/A	NP_001351228.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OXCT1	ENST00000196371.10	TSL:1 MANE Select	c.78+14dupG	intron	N/A	ENSP00000196371.5	P55809-1
OXCT1	ENST00000972071.1		c.78+14dupG	intron	N/A	ENSP00000642130.1
OXCT1	ENST00000919063.1		c.78+14dupG	intron	N/A	ENSP00000589122.1

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

GnomAD2 exomes

AF:

0.0313

AC:

7843

AN:

250232

AF XY:

0.0296

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 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

African (AFR)

AF:

0.00165

AC:

AN:

33382

American (AMR)

AF:

0.122

AC:

5462

AN:

44688

Ashkenazi Jewish (ASJ)

AF:

0.000460

AC:

AN:

26088

East Asian (EAS)

AF:

0.0368

AC:

1459

AN:

39672

South Asian (SAS)

AF:

0.0716

AC:

6164

AN:

86102

European-Finnish (FIN)

AF:

0.0205

AC:

1096

AN:

53404

Middle Eastern (MID)

AF:

0.00625

AC:

AN:

5758

European-Non Finnish (NFE)

AF:

0.000447

AC:

495

AN:

1107266

Other (OTH)

AF:

0.0126

AC:

760

AN:

60180

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

965

1930

2894

3859

4824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

194

388

582

776

970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0142

AC:

2160

AN:

152134

Hom.:

100

Cov.:

AF XY:

0.0175

AC XY:

1298

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.00279

AC:

116

AN:

41520

American (AMR)

AF:

0.0759

AC:

1160

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.000576

AC:

AN:

3472

East Asian (EAS)

AF:

0.0314

AC:

161

AN:

5134

South Asian (SAS)

AF:

0.0783

AC:

377

AN:

4816

European-Finnish (FIN)

AF:

0.0224

AC:

238

AN:

10604

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00103

AC:

AN:

67986

Other (OTH)

AF:

0.0161

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

198

296

395

494

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00558

Hom.:

Bravo

AF:

0.0168

Asia WGS

AF:

0.0500

AC:

174

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Succinyl-CoA acetoacetate transferase deficiency (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.67

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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5-41870266-TCCC-TCCCC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over