Variant rs1258184 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_018245.3(OGDHL):c.564C>T(p.Leu188=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,613,382 control chromosomes in the GnomAD database, including 193,363 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.41 ( 14875 hom., cov: 32)

Exomes 𝑓: 0.48 ( 178488 hom. )

Consequence

OGDHL
NM_018245.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.99

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 10-49752163-G-A is Benign according to our data. Variant chr10-49752163-G-A is described in ClinVar as [Benign]. Clinvar id is 3059593.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.99 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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.564C>T	p.Leu188=	synonymous_variant	5/23	ENST00000374103.9	NP_060715.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OGDHL	ENST00000374103.9 linkuse as main transcript	c.564C>T	p.Leu188=	synonymous_variant	5/23	1	NM_018245.3	ENSP00000363216	P1	Q9ULD0-1
OGDHL	ENST00000419399.4 linkuse as main transcript	c.393C>T	p.Leu131=	synonymous_variant	4/22	2		ENSP00000401356		Q9ULD0-2
OGDHL	ENST00000432695.2 linkuse as main transcript	c.-64C>T		5_prime_UTR_variant	3/21	2		ENSP00000390240		Q9ULD0-3

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62596

AN:

151936

Hom.:

14876

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.534

Gnomad AMR

AF:

0.486

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.888

Gnomad SAS

AF:

0.426

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.422

GnomAD3 exomes

AF:

0.489

AC:

122670

AN:

251048

Hom.:

32572

AF XY:

0.483

AC XY:

65599

AN XY:

135692

show subpopulations

Gnomad AFR exome

AF:

0.182

Gnomad AMR exome

AF:

0.548

Gnomad ASJ exome

AF:

0.335

Gnomad EAS exome

AF:

0.891

Gnomad SAS exome

AF:

0.413

Gnomad FIN exome

AF:

0.510

Gnomad NFE exome

AF:

0.481

Gnomad OTH exome

AF:

0.463

GnomAD4 exome

AF:

0.485

AC:

708694

AN:

1461328

Hom.:

178488

Cov.:

AF XY:

0.481

AC XY:

350030

AN XY:

726986

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.541

Gnomad4 ASJ exome

AF:

0.332

Gnomad4 EAS exome

AF:

0.885

Gnomad4 SAS exome

AF:

0.411

Gnomad4 FIN exome

AF:

0.513

Gnomad4 NFE exome

AF:

0.487

Gnomad4 OTH exome

AF:

0.469

GnomAD4 genome

AF:

0.412

AC:

62608

AN:

152054

Hom.:

14875

Cov.:

AF XY:

0.415

AC XY:

30858

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.188

Gnomad4 AMR

AF:

0.486

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.888

Gnomad4 SAS

AF:

0.427

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.481

Gnomad4 OTH

AF:

0.426

Alfa

AF:

0.451

Hom.:

18826

Bravo

AF:

0.405

Asia WGS

AF:

0.640

AC:

2224

AN:

3478

EpiCase

AF:

0.467

EpiControl

AF:

0.463

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

OGDHL-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 11, 2021

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

-0.70

CADD

Benign

2.0

DANN

Benign

0.65

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