15-90102783-TC-T

Variant names:

• chr15-90102783-TC-T
• rs139195728
• ENST00000824298.1:n.182delC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000824298.1(IDH2-DT):​n.182delC 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 0.0263 in 156,056 control chromosomes in the GnomAD database, including 197 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.027 (196 hom., cov: 32)
  • Exomes 𝑓: 0.0064 (1 hom.)
• Consequence: IDH2-DT ENST00000824298.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.514
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 15-90102783-TC-T is Benign according to our data. Variant chr15-90102783-TC-T is described in ClinVar as Benign. ClinVar VariationId is 1244495.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824298.1. 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.247+406delC		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDH2-DT	ENST00000824298.1		n.182delC		non_coding_transcript_exon	Exon 1 of 2
	IDH2-DT	ENST00000561101.3	TSL:3	n.115+21delC		intron	N/A
	IDH2-DT	ENST00000824295.1		n.142+21delC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0267 AC: 4061 AN: 152166 Hom.: 194 Cov.: 32

Gnomad AFR AF: 0.0933

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00923

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.0177

GnomAD4 exome AF: 0.00636 AC: 24 AN: 3772 Hom.: 1 Cov.: 0 AF XY: 0.00660 AC XY: 12 AN XY: 1818

African (AFR) AF: 0.0882 AC: 15 AN: 170

American (AMR) AF: 0.0351 AC: 4 AN: 114

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 236

East Asian (EAS) AF: 0.00 AC: 0 AN: 420

South Asian (SAS) AF: 0.00 AC: 0 AN: 38

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44

Middle Eastern (MID) AF: 0.0357 AC: 1 AN: 28

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2382

Other (OTH) AF: 0.0118 AC: 4 AN: 340

GnomAD4 genome AF: 0.0268 AC: 4079 AN: 152284 Hom.: 196 Cov.: 32 AF XY: 0.0256 AC XY: 1905 AN XY: 74472

African (AFR) AF: 0.0935 AC: 3887 AN: 41568

American (AMR) AF: 0.00915 AC: 140 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000206 AC: 14 AN: 68006

Other (OTH) AF: 0.0175 AC: 37 AN: 2114

Alfa AF: 0.000817 Hom.: 0

Bravo AF: 0.0310

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs139195728; hg19: chr15-90646015;