rs11632348

Variant names:

• chr15-90104814-C-A
• rs11632348
• ENST00000561101.3:n.188+1362C>A

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+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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 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+1362C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDH2-DT	ENST00000561101.3	TSL:3	n.188+1362C>A		intron	N/A
	IDH2-DT	ENST00000824295.1		n.215+1362C>A		intron	N/A
	IDH2-DT	ENST00000824296.1		n.171+2051C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68852 AN: 151974 Hom.: 16737 Cov.: 33

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.: 33 AF XY: 0.447 AC XY: 33194 AN XY: 74342

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.4
DANN	Benign	0.74
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs11632348; hg19: chr15-90648046;