dbSNP rs2229434: INSR:p.Thr816Thr (chr19-7142910-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_000208.4(INSR):c.2448G>A(p.Thr816Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00924 in 1,614,044 control chromosomes in the GnomAD database, including 156 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 45 hom., cov: 32)

Exomes 𝑓: 0.0083 ( 111 hom. )

Consequence

INSR
NM_000208.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -2.57

Publications

12 publications found

Variant links:

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]

INSR Gene-Disease associations (from GenCC):

insulin-resistance syndrome type A
Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet, G2P
Donohue syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P, Orphanet
hyperinsulinism due to INSR deficiency
Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
Rabson-Mendenhall syndrome
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)

INSR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 19-7142910-C-T is Benign according to our data. Variant chr19-7142910-C-T is described in ClinVar as Benign. ClinVar VariationId is 330460.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.57 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.018 (2732/152194) while in subpopulation AFR AF = 0.042 (1743/41526). AF 95% confidence interval is 0.0403. There are 45 homozygotes in GnomAd4. There are 1327 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 45 AR,AD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000208.4. 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
	INSR	NM_000208.4	MANE Select	c.2448G>A	p.Thr816Thr	synonymous	Exon 12 of 22	NP_000199.2	P06213-1
	INSR	NM_001079817.3		c.2412G>A	p.Thr804Thr	synonymous	Exon 11 of 21	NP_001073285.1	P06213-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
INSR	ENST00000302850.10	TSL:1 MANE Select	c.2448G>A	p.Thr816Thr	synonymous	Exon 12 of 22	ENSP00000303830.4	P06213-1
INSR	ENST00000341500.9	TSL:1	c.2412G>A	p.Thr804Thr	synonymous	Exon 11 of 21	ENSP00000342838.4	P06213-2
INSR	ENST00000904791.1		c.2448G>A	p.Thr816Thr	synonymous	Exon 12 of 22	ENSP00000574850.1

Frequencies

GnomAD3 genomes

AF:

0.0179

AC:

2717

AN:

152076

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0417

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.00721

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.0418

Gnomad SAS

AF:

0.00414

Gnomad FIN

AF:

0.00943

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00666

Gnomad OTH

AF:

0.0159

GnomAD2 exomes

AF:

0.0112

AC:

2809

AN:

251192

AF XY:

0.00992

show subpopulations

Gnomad AFR exome

AF:

0.0436

Gnomad AMR exome

AF:

0.00431

Gnomad ASJ exome

AF:

0.0118

Gnomad EAS exome

AF:

0.0392

Gnomad FIN exome

AF:

0.0101

Gnomad NFE exome

AF:

0.00679

Gnomad OTH exome

AF:

0.00962

GnomAD4 exome

AF:

0.00833

AC:

12182

AN:

1461850

Hom.:

111

Cov.:

AF XY:

0.00793

AC XY:

5769

AN XY:

727236

show subpopulations

African (AFR)

AF:

0.0405

AC:

1357

AN:

33476

American (AMR)

AF:

0.00456

AC:

204

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

339

AN:

26134

East Asian (EAS)

AF:

0.0418

AC:

1660

AN:

39694

South Asian (SAS)

AF:

0.00226

AC:

195

AN:

86250

European-Finnish (FIN)

AF:

0.0105

AC:

562

AN:

53412

Middle Eastern (MID)

AF:

0.00954

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00644

AC:

7161

AN:

1112004

Other (OTH)

AF:

0.0107

AC:

649

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

752

1504

2257

3009

3761

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

326

652

978

1304

1630

<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:

0.0180

AC:

2732

AN:

152194

Hom.:

Cov.:

AF XY:

0.0178

AC XY:

1327

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.0420

AC:

1743

AN:

41526

American (AMR)

AF:

0.00720

AC:

110

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0153

AC:

AN:

3468

East Asian (EAS)

AF:

0.0415

AC:

215

AN:

5176

South Asian (SAS)

AF:

0.00415

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00943

AC:

100

AN:

10610

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00666

AC:

453

AN:

68006

Other (OTH)

AF:

0.0157

AC:

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

129

257

386

514

643

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.0105

Hom.:

Bravo

AF:

0.0196

Asia WGS

AF:

0.0230

AC:

AN:

3478

EpiCase

AF:

0.00529

EpiControl

AF:

0.00516

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Insulin-resistant diabetes mellitus AND acanthosis nigricans (1)

Leprechaunism syndrome (1)

Rabson-Mendenhall syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

1.2

(source)

DANN

Benign

0.74

PhyloP100

-2.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

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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