19-7114277-C-T

Position:

• chr19-7114277-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000208.4(INSR):​c.*2779G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,046 control chromosomes in the GnomAD database, including 34,940 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.68 (34930 hom., cov: 31)
  • Exomes 𝑓: 0.60 (10 hom.)
• Consequence: INSR NM_000208.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -1.48

Genes affected

INSR (HGNC:6091): (insulin receptor) This gene encodes a member of the receptor tyrosine kinase family of proteins. The encoded preproprotein is proteolytically processed to generate alpha and beta subunits that form a heterotetrameric receptor. Binding of insulin or other ligands to this receptor activates the insulin signaling pathway, which regulates glucose uptake and release, as well as the synthesis and storage of carbohydrates, lipids and protein. Mutations in this gene underlie the inherited severe insulin resistance syndromes including type A insulin resistance syndrome, Donohue syndrome and Rabson-Mendenhall syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 19-7114277-C-T is Benign according to our data. Variant chr19-7114277-C-T is described in ClinVar as [Benign]. Clinvar id is 330380.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INSR	NM_000208.4	c.*2779G>A		3_prime_UTR_variant	22/22	ENST00000302850.10	NP_000199.2
INSR	NM_001079817.3	c.*2779G>A		3_prime_UTR_variant	21/21		NP_001073285.1
INSR	XM_011527988.3	c.*2779G>A		3_prime_UTR_variant	22/22		XP_011526290.2
INSR	XM_011527989.4	c.*2779G>A		3_prime_UTR_variant	21/21		XP_011526291.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INSR	ENST00000302850	c.*2779G>A		3_prime_UTR_variant	22/22	1	NM_000208.4	ENSP00000303830.4
INSR	ENST00000341500	c.*2779G>A		3_prime_UTR_variant	21/21	1		ENSP00000342838.4

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102474 AN: 151876 Hom.: 34867 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.644

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.674

GnomAD4 exome AF: 0.596 AC: 31 AN: 52 Hom.: 10 Cov.: 0 AF XY: 0.595 AC XY: 25 AN XY: 42

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.587

GnomAD4 genome AF: 0.675 AC: 102600 AN: 151994 Hom.: 34930 Cov.: 31 AF XY: 0.678 AC XY: 50336 AN XY: 74290

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.676

Alfa AF: 0.643 Hom.: 31415

Bravo AF: 0.684

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Insulin-resistant diabetes mellitus AND acanthosis nigricans Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Rabson-Mendenhall syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Leprechaunism syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3745551; hg19: chr19-7114288;