Variant rs6107100 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The NM_006899.5(IDH3B):c.37-34G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,612,784 control chromosomes in the GnomAD database, including 13,565 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 3778 hom., cov: 32)

Exomes 𝑓: 0.099 ( 9787 hom. )

Consequence

IDH3B
NM_006899.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0560

Variant links:

Genes affected

IDH3B (HGNC:5385): (isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit beta) Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. NAD(+)-dependent isocitrate dehydrogenases catalyze the allosterically regulated rate-limiting step of the tricarboxylic acid cycle. Each isozyme is a heterotetramer that is composed of two alpha subunits, one beta subunit, and one gamma subunit. The protein encoded by this gene is the beta subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Sep 2016]

IDH3B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 20-2664039-C-A is Benign according to our data. Variant chr20-2664039-C-A is described in ClinVar as [Benign]. Clinvar id is 1276882.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IDH3B	NM_006899.5 linkuse as main transcript	c.37-34G>T		intron_variant		ENST00000380843.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IDH3B	ENST00000380843.9 linkuse as main transcript	c.37-34G>T		intron_variant		1	NM_006899.5		O43837-1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26532

AN:

152064

Hom.:

3780

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.0395

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.0786

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0784

Gnomad OTH

AF:

0.154

GnomAD3 exomes

AF:

0.134

AC:

33343

AN:

249532

Hom.:

3253

AF XY:

0.125

AC XY:

16844

AN XY:

135192

show subpopulations

Gnomad AFR exome

AF:

0.394

Gnomad AMR exome

AF:

0.202

Gnomad ASJ exome

AF:

0.0436

Gnomad EAS exome

AF:

0.229

Gnomad SAS exome

AF:

0.138

Gnomad FIN exome

AF:

0.0838

Gnomad NFE exome

AF:

0.0786

Gnomad OTH exome

AF:

0.101

GnomAD4 exome

AF:

0.0985

AC:

143879

AN:

1460602

Hom.:

9787

Cov.:

AF XY:

0.0978

AC XY:

71095

AN XY:

726722

show subpopulations

Gnomad4 AFR exome

AF:

0.402

Gnomad4 AMR exome

AF:

0.193

Gnomad4 ASJ exome

AF:

0.0446

Gnomad4 EAS exome

AF:

0.233

Gnomad4 SAS exome

AF:

0.136

Gnomad4 FIN exome

AF:

0.0856

Gnomad4 NFE exome

AF:

0.0787

Gnomad4 OTH exome

AF:

0.117

GnomAD4 genome

AF:

0.175

AC:

26564

AN:

152182

Hom.:

3778

Cov.:

AF XY:

0.173

AC XY:

12860

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.383

Gnomad4 AMR

AF:

0.140

Gnomad4 ASJ

AF:

0.0395

Gnomad4 EAS

AF:

0.221

Gnomad4 SAS

AF:

0.150

Gnomad4 FIN

AF:

0.0786

Gnomad4 NFE

AF:

0.0784

Gnomad4 OTH

AF:

0.154

Alfa

AF:

0.101

Hom.:

396

Bravo

AF:

0.191

Asia WGS

AF:

0.227

AC:

791

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

5.3

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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