Variant 20-2664431-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The ENST00000418739.1(IDH3B-DT):n.80G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0931 in 621,352 control chromosomes in the GnomAD database, including 3,480 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.078 ( 656 hom., cov: 33)

Exomes 𝑓: 0.098 ( 2824 hom. )

Consequence

IDH3B-DT
ENST00000418739.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.221

Variant links:

Genes affected

IDH3B-DT (HGNC:):

IDH3B-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 20-2664431-G-A is Benign according to our data. Variant chr20-2664431-G-A is described in ClinVar as [Benign]. Clinvar id is 1271565.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IDH3B-DT	NR_186432.1 linkuse as main transcript	n.158G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IDH3B-DT	ENST00000418739.1 linkuse as main transcript	n.80G>A		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes

AF:

0.0780

AC:

11869

AN:

152110

Hom.:

662

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0490

Gnomad AMI

AF:

0.0242

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.0346

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.144

Gnomad FIN

AF:

0.0788

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0780

Gnomad OTH

AF:

0.0831

GnomAD4 exome

AF:

0.0980

AC:

45989

AN:

469122

Hom.:

2824

Cov.:

AF XY:

0.0992

AC XY:

24614

AN XY:

248170

show subpopulations

Gnomad4 AFR exome

AF:

0.0496

Gnomad4 AMR exome

AF:

0.159

Gnomad4 ASJ exome

AF:

0.0415

Gnomad4 EAS exome

AF:

0.231

Gnomad4 SAS exome

AF:

0.129

Gnomad4 FIN exome

AF:

0.0841

Gnomad4 NFE exome

AF:

0.0794

Gnomad4 OTH exome

AF:

0.0960

GnomAD4 genome

AF:

0.0780

AC:

11869

AN:

152230

Hom.:

656

Cov.:

AF XY:

0.0794

AC XY:

5909

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0489

Gnomad4 AMR

AF:

0.0997

Gnomad4 ASJ

AF:

0.0346

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.143

Gnomad4 FIN

AF:

0.0788

Gnomad4 NFE

AF:

0.0780

Gnomad4 OTH

AF:

0.0841

Alfa

AF:

0.0772

Hom.:

Bravo

AF:

0.0815

Asia WGS

AF:

0.203

AC:

705

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.44

CADD

Benign

4.0

DANN

Benign

0.87

Splicing

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