chr10-92565754-C-T

Variant names:

• chr10-92565754-C-T
• rs7076966
• NM_004969.4:c.98+8168G>A

Variant summary

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

The NM_004969.4(IDE):​c.98+8168G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,004 control chromosomes in the GnomAD database, including 11,955 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 0.37 (11955 hom., cov: 31)
• Consequence: IDE NM_004969.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 4 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IDE	NM_004969.4	c.98+8168G>A		intron_variant	Intron 1 of 24	ENST00000265986.11	NP_004960.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IDE	ENST00000265986.11	c.98+8168G>A		intron_variant	Intron 1 of 24	1	NM_004969.4	ENSP00000265986.6

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56725 AN: 151884 Hom.: 11959 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.373 AC: 56733 AN: 152004 Hom.: 11955 Cov.: 31 AF XY: 0.376 AC XY: 27908 AN XY: 74302

African (AFR) AF: 0.186 AC: 7701 AN: 41486

American (AMR) AF: 0.325 AC: 4959 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1998 AN: 3472

East Asian (EAS) AF: 0.671 AC: 3465 AN: 5162

South Asian (SAS) AF: 0.519 AC: 2497 AN: 4810

European-Finnish (FIN) AF: 0.440 AC: 4649 AN: 10558

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30006 AN: 67948

Other (OTH) AF: 0.397 AC: 838 AN: 2110

Alfa AF: 0.393 Hom.: 2105

Bravo AF: 0.359

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.9
DANN	Benign	0.88
PhyloP100		-0.085
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: rs7076966; hg19: chr10-94325511;