rs4932158

Variant names:

• chr15-90106171-A-G
• rs4932158
• ENST00000561101.3:n.188+2719A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-90106171-A-G
• chr15-90106171-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561101.3(IDH2-DT):​n.188+2719A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 150,920 control chromosomes in the GnomAD database, including 51,572 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 0.82 (51572 hom., cov: 27)
• Consequence: IDH2-DT ENST00000561101.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561101.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDH2-DT	NR_149130.1		n.320+2719A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDH2-DT	ENST00000561101.3	TSL:3	n.188+2719A>G		intron	N/A
	IDH2-DT	ENST00000824295.1		n.215+2719A>G		intron	N/A
	IDH2-DT	ENST00000824296.1		n.171+3408A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 123846 AN: 150806 Hom.: 51523 Cov.: 27

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.821 AC: 123952 AN: 150920 Hom.: 51572 Cov.: 27 AF XY: 0.817 AC XY: 60138 AN XY: 73616

African (AFR) AF: 0.927 AC: 38127 AN: 41114

American (AMR) AF: 0.728 AC: 10996 AN: 15102

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2882 AN: 3464

East Asian (EAS) AF: 0.466 AC: 2353 AN: 5054

South Asian (SAS) AF: 0.714 AC: 3385 AN: 4744

European-Finnish (FIN) AF: 0.837 AC: 8670 AN: 10356

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 54881 AN: 67796

Other (OTH) AF: 0.801 AC: 1674 AN: 2090

Alfa AF: 0.827 Hom.: 6092

Bravo AF: 0.815

Asia WGS AF: 0.618 AC: 2144 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.27
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4932158; hg19: chr15-90649403;