dbSNP rs11632348: IDH2-DT:n.188+1362C>A (chr15-90104814-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000561101.3(IDH2-DT):n.188+1362C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,092 control chromosomes in the GnomAD database, including 16,743 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 0.45 ( 16743 hom., cov: 33)

Consequence

IDH2-DT
ENST00000561101.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.518

Publications

7 publications found

Variant links:

Genes affected

IDH2-DT (HGNC:53154): (IDH2 divergent transcript)

IDH2-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IDH2-DT	NR_149130.1 link	n.320+1362C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
IDH2-DT	ENST00000561101.3 link	n.188+1362C>A	intron_variant	Intron 2 of 4	3
IDH2-DT	ENST00000824295.1 link	n.215+1362C>A	intron_variant	Intron 2 of 3
IDH2-DT	ENST00000824296.1 link	n.171+2051C>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.453

AC:

68852

AN:

151974

Hom.:

16737

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.528

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.560

Gnomad OTH

AF:

0.446

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.453

AC:

68907

AN:

152092

Hom.:

16743

Cov.:

AF XY:

0.447

AC XY:

33194

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.295

AC:

12234

AN:

41468

American (AMR)

AF:

0.448

AC:

6847

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.467

AC:

1618

AN:

3468

East Asian (EAS)

AF:

0.258

AC:

1336

AN:

5184

South Asian (SAS)

AF:

0.321

AC:

1551

AN:

4828

European-Finnish (FIN)

AF:

0.528

AC:

5584

AN:

10578

Middle Eastern (MID)

AF:

0.442

AC:

130

AN:

294

European-Non Finnish (NFE)

AF:

0.560

AC:

38081

AN:

67964

Other (OTH)

AF:

0.445

AC:

940

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1859

3717

5576

7434

9293

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

616

1232

1848

2464

3080

<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:

0.500

Hom.:

10099

Bravo

AF:

0.442

Asia WGS

AF:

0.297

AC:

1031

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.4

(source)

DANN

Benign

0.74

PhyloP100

0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over