Genetic Variant IDE:c.1740-195_1740-190delACACAC (chr10-92479610-AGTGTGT-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004969.4(IDE):c.1740-195_1740-190delACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000291 in 470,194 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00062 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

IDE
NM_004969.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.969

Publications

1 publications found

Variant links:

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]

IDE links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IDE	NM_004969.4	MANE Select	c.1740-195_1740-190delACACAC	intron	N/A	NP_004960.2
IDE	NM_001322793.2		c.1740-827_1740-822delACACAC	intron	N/A	NP_001309722.1
IDE	NM_001322794.2		c.1623-195_1623-190delACACAC	intron	N/A	NP_001309723.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IDE	ENST00000265986.11	TSL:1 MANE Select	c.1740-195_1740-190delACACAC	intron	N/A	ENSP00000265986.6
IDE	ENST00000478361.6	TSL:1	n.2074-195_2074-190delACACAC	intron	N/A	ENSP00000473506.1
IDE	ENST00000679069.1		n.3117_3122delACACAC	non_coding_transcript_exon	Exon 15 of 25

Frequencies

GnomAD3 genomes

AF:

0.000619

AC:

AN:

150182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00207

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000665

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000582

Gnomad SAS

AF:

0.000210

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000445

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000138

AC:

AN:

319914

Hom.:

AF XY:

0.000120

AC XY:

AN XY:

167256

show subpopulations

African (AFR)

AF:

0.000803

AC:

AN:

9968

American (AMR)

AF:

0.0000697

AC:

AN:

14348

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10204

East Asian (EAS)

AF:

0.000622

AC:

AN:

22498

South Asian (SAS)

AF:

0.000263

AC:

AN:

26618

European-Finnish (FIN)

AF:

0.0000460

AC:

AN:

21734

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1418

European-Non Finnish (NFE)

AF:

0.0000309

AC:

AN:

194002

Other (OTH)

AF:

0.000366

AC:

AN:

19124

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.439

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000619

AC:

AN:

150280

Hom.:

Cov.:

AF XY:

0.000641

AC XY:

AN XY:

73350

show subpopulations

African (AFR)

AF:

0.00207

AC:

AN:

41074

American (AMR)

AF:

0.0000664

AC:

AN:

15064

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3410

East Asian (EAS)

AF:

0.000583

AC:

AN:

5146

South Asian (SAS)

AF:

0.000210

AC:

AN:

4756

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10158

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0000445

AC:

AN:

67398

Other (OTH)

AF:

0.00

AC:

AN:

2078

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.97

Splicing

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

Publications

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10-92479610-AGTGTGTGTGTGT-AGTGTGT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over