10-92452778-T-TG

Variant names:

• chr10-92452778-T-TG
• rs5786996
• NM_004969.4:c.*1665dupC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_004969.4(IDE):​c.*1665dupC variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0339 in 152,322 control chromosomes in the GnomAD database, including 137 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.034 (137 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IDE NM_004969.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.67
• Publications: 6 publications found

Genes affected

IDE (HGNC:5381): (insulin degrading enzyme) This gene encodes a zinc metallopeptidase that degrades intracellular insulin, and thereby terminates insulins activity, as well as participating in intercellular peptide signalling by degrading diverse peptides such as glucagon, amylin, bradykinin, and kallidin. The preferential affinity of this enzyme for insulin results in insulin-mediated inhibition of the degradation of other peptides such as beta-amyloid. Deficiencies in this protein's function are associated with Alzheimer's disease and type 2 diabetes mellitus but mutations in this gene have not been shown to be causitive for these diseases. This protein localizes primarily to the cytoplasm but in some cell types localizes to the extracellular space, cell membrane, peroxisome, and mitochondrion. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants have been described but have not been experimentally verified.[provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004969.4. 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
	IDE	NM_004969.4	MANE Select	c.*1665dupC		3_prime_UTR	Exon 25 of 25	NP_004960.2	P14735-1
	IDE	NM_001322793.2		c.*1665dupC		3_prime_UTR	Exon 25 of 25	NP_001309722.1	A0A3B3ISG5
	IDE	NM_001322794.2		c.*1665dupC		3_prime_UTR	Exon 25 of 25	NP_001309723.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDE	ENST00000265986.11	TSL:1 MANE Select	c.*1665dupC		3_prime_UTR	Exon 25 of 25	ENSP00000265986.6	P14735-1
	IDE	ENST00000971392.1		c.*1665dupC		3_prime_UTR	Exon 26 of 26	ENSP00000641451.1
	IDE	ENST00000857320.1		c.*1665dupC		3_prime_UTR	Exon 26 of 26	ENSP00000527379.1

Frequencies

GnomAD3 genomes AF: 0.0340 AC: 5170 AN: 152204 Hom.: 137 Cov.: 32

Gnomad AFR AF: 0.00943

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0210

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0339 AC: 5168 AN: 152322 Hom.: 137 Cov.: 32 AF XY: 0.0359 AC XY: 2675 AN XY: 74486

African (AFR) AF: 0.00940 AC: 391 AN: 41592

American (AMR) AF: 0.0578 AC: 884 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3468

East Asian (EAS) AF: 0.0395 AC: 205 AN: 5192

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4822

European-Finnish (FIN) AF: 0.0818 AC: 868 AN: 10610

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0388 AC: 2641 AN: 68028

Other (OTH) AF: 0.0208 AC: 44 AN: 2116

Alfa AF: 0.0396 Hom.: 14

Bravo AF: 0.0310

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5786996; hg19: chr10-94212535;