chr10-92494526-A-G

Variant names:

• chr10-92494526-A-G
• rs1855916
• NM_004969.4:c.1431-3931T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004969.4(IDE):​c.1431-3931T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,014 control chromosomes in the GnomAD database, including 55,251 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 0.85 (55251 hom., cov: 30)
• Consequence: IDE NM_004969.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDE	NM_004969.4	MANE Select	c.1431-3931T>C		intron	N/A	NP_004960.2
	IDE	NM_001322793.2		c.1431-3931T>C		intron	N/A	NP_001309722.1
	IDE	NM_001322794.2		c.1314-3931T>C		intron	N/A	NP_001309723.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDE	ENST00000265986.11	TSL:1 MANE Select	c.1431-3931T>C		intron	N/A	ENSP00000265986.6
	IDE	ENST00000478361.6	TSL:1	n.*1641-3931T>C		intron	N/A	ENSP00000473506.1
	IDE	ENST00000650060.2		c.1431-3931T>C		intron	N/A	ENSP00000497272.1

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129238 AN: 151896 Hom.: 55206 Cov.: 30

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.827

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.851 AC: 129341 AN: 152014 Hom.: 55251 Cov.: 30 AF XY: 0.851 AC XY: 63247 AN XY: 74302

African (AFR) AF: 0.920 AC: 38144 AN: 41472

American (AMR) AF: 0.815 AC: 12445 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3047 AN: 3472

East Asian (EAS) AF: 0.936 AC: 4821 AN: 5150

South Asian (SAS) AF: 0.841 AC: 4049 AN: 4812

European-Finnish (FIN) AF: 0.862 AC: 9096 AN: 10554

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54978 AN: 67970

Other (OTH) AF: 0.825 AC: 1740 AN: 2108

Alfa AF: 0.834 Hom.: 6844

Bravo AF: 0.851

Asia WGS AF: 0.880 AC: 3058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1855916; hg19: chr10-94254283;