15-90106171-A-G

Position:

• chr15-90106171-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_149130.1(IDH2-DT):​n.320+2719A>G variant causes a intron, non coding transcript 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 NR_149130.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IDH2-DT	NR_149130.1	n.320+2719A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IDH2-DT	ENST00000561101.3	n.188+2719A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.801

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4932158; hg19: chr15-90649403;