Variant rs7090775 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001347826.1(OGDHL):c.-270G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 1,614,154 control chromosomes in the GnomAD database, including 1,427 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.040 ( 169 hom., cov: 32)

Exomes 𝑓: 0.036 ( 1258 hom. )

Consequence

OGDHL
NM_001347826.1 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.48

Variant links:

Genes affected

OGDHL (HGNC:25590): (oxoglutarate dehydrogenase L) The protein encoded by this gene is similar to oxoglutarate dehydrogenase (OGDH) of the OGDH complex, which degrades glucose and glutamate. This gene encodes several isoforms, including some that appear to localize to mitochondria. The encoded protein down-regulates the AKT signaling cascade and can suppress the growth of cervical cancer cells. [provided by RefSeq, Dec 2016]

OGDHL links:

OGDHL (HGNC:):

OGDHL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OGDHL	NM_018245.3 linkuse as main transcript	c.657G>A	p.Gln219Gln	synonymous_variant	6/23	ENST00000374103.9	NP_060715.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
OGDHL	ENST00000374103.9 linkuse as main transcript	c.657G>A	p.Gln219Gln	synonymous_variant	6/23	1	NM_018245.3	ENSP00000363216.4	Q9ULD0-1
OGDHL	ENST00000419399.4 linkuse as main transcript	c.486G>A	p.Gln162Gln	synonymous_variant	5/22	2		ENSP00000401356.1	Q9ULD0-2
OGDHL	ENST00000432695.2 linkuse as main transcript	c.30G>A	p.Gln10Gln	synonymous_variant	4/21	2		ENSP00000390240.1	Q9ULD0-3

Frequencies

GnomAD3 genomes

AF:

0.0398

AC:

6052

AN:

152200

Hom.:

164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0614

Gnomad AMI

AF:

0.0187

Gnomad AMR

AF:

0.0289

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.0938

Gnomad FIN

AF:

0.0242

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0319

Gnomad OTH

AF:

0.0368

GnomAD3 exomes

AF:

0.0368

AC:

9264

AN:

251466

Hom.:

285

AF XY:

0.0401

AC XY:

5454

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0645

Gnomad AMR exome

AF:

0.0195

Gnomad ASJ exome

AF:

0.0214

Gnomad EAS exome

AF:

0.00332

Gnomad SAS exome

AF:

0.0972

Gnomad FIN exome

AF:

0.0240

Gnomad NFE exome

AF:

0.0310

Gnomad OTH exome

AF:

0.0393

GnomAD4 exome

AF:

0.0364

AC:

53199

AN:

1461836

Hom.:

1258

Cov.:

AF XY:

0.0379

AC XY:

27539

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.0612

Gnomad4 AMR exome

AF:

0.0207

Gnomad4 ASJ exome

AF:

0.0206

Gnomad4 EAS exome

AF:

0.00184

Gnomad4 SAS exome

AF:

0.0927

Gnomad4 FIN exome

AF:

0.0243

Gnomad4 NFE exome

AF:

0.0337

Gnomad4 OTH exome

AF:

0.0407

GnomAD4 genome

AF:

0.0399

AC:

6084

AN:

152318

Hom.:

169

Cov.:

AF XY:

0.0400

AC XY:

2978

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.0620

Gnomad4 AMR

AF:

0.0288

Gnomad4 ASJ

AF:

0.0173

Gnomad4 EAS

AF:

0.00289

Gnomad4 SAS

AF:

0.0938

Gnomad4 FIN

AF:

0.0242

Gnomad4 NFE

AF:

0.0319

Gnomad4 OTH

AF:

0.0369

Alfa

AF:

0.0340

Hom.:

Bravo

AF:

0.0401

Asia WGS

AF:

0.0600

AC:

210

AN:

3478

EpiCase

AF:

0.0310

EpiControl

AF:

0.0351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

9.8

DANN

Benign

0.78

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over