rs3194051

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002185.5(IL7R):c.1066A>G(p.Ile356Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,613,732 control chromosomes in the GnomAD database, including 55,069 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

Frequency

Genomes: 𝑓 0.28 ( 6159 hom., cov: 31)

Exomes 𝑓: 0.25 ( 48910 hom. )

Consequence

IL7R
NM_002185.5 missense

Scores

Clinical Significance

Benign reviewed by expert panel B:6O:2

Conservation

PhyloP100: 1.06

Variant links:

Genes affected

IL7R (HGNC:6024): (interleukin 7 receptor) The protein encoded by this gene is a receptor for interleukin 7 (IL7). The function of this receptor requires the interleukin 2 receptor, gamma chain (IL2RG), which is a common gamma chain shared by the receptors of various cytokines, including interleukins 2, 4, 7, 9, and 15. This protein has been shown to play a critical role in V(D)J recombination during lymphocyte development. Defects in this gene may be associated with severe combined immunodeficiency (SCID). Alternatively spliced transcript variants have been found. [provided by RefSeq, Dec 2015]

IL7R links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0043572485).

BP6

Variant 5-35876172-A-G is Benign according to our data. Variant chr5-35876172-A-G is described in ClinVar as [Benign]. Clinvar id is 134533.Status of the report is reviewed_by_expert_panel, 3 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
IL7R	NM_002185.5 linkuse as main transcript	c.1066A>G	p.Ile356Val	missense_variant	8/8	ENST00000303115.8
IL7R	NM_001410734.1 linkuse as main transcript	c.*183A>G		3_prime_UTR_variant	7/7
IL7R	NR_120485.3 linkuse as main transcript	n.890A>G		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL7R	ENST00000303115.8 linkuse as main transcript	c.1066A>G	p.Ile356Val	missense_variant	8/8	1	NM_002185.5	P1	P16871-1
IL7R	ENST00000505093.1 linkuse as main transcript	c.*183A>G		3_prime_UTR_variant	3/3	2
IL7R	ENST00000505875.1 linkuse as main transcript	n.364A>G		non_coding_transcript_exon_variant	2/2	2
IL7R	ENST00000514217.5 linkuse as main transcript	c.*260A>G		3_prime_UTR_variant, NMD_transcript_variant	6/6	2

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42072

AN:

151874

Hom.:

6159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.264

Gnomad EAS

AF:

0.0724

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.275

GnomAD3 exomes

AF:

0.239

AC:

59865

AN:

250888

Hom.:

7907

AF XY:

0.242

AC XY:

32748

AN XY:

135586

show subpopulations

Gnomad AFR exome

AF:

0.348

Gnomad AMR exome

AF:

0.147

Gnomad ASJ exome

AF:

0.272

Gnomad EAS exome

AF:

0.0673

Gnomad SAS exome

AF:

0.206

Gnomad FIN exome

AF:

0.296

Gnomad NFE exome

AF:

0.272

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

AF:

0.254

AC:

371947

AN:

1461740

Hom.:

48910

Cov.:

AF XY:

0.254

AC XY:

184696

AN XY:

727172

show subpopulations

Gnomad4 AFR exome

AF:

0.342

Gnomad4 AMR exome

AF:

0.158

Gnomad4 ASJ exome

AF:

0.272

Gnomad4 EAS exome

AF:

0.0707

Gnomad4 SAS exome

AF:

0.207

Gnomad4 FIN exome

AF:

0.293

Gnomad4 NFE exome

AF:

0.264

Gnomad4 OTH exome

AF:

0.245

GnomAD4 genome

AF:

0.277

AC:

42076

AN:

151992

Hom.:

6159

Cov.:

AF XY:

0.275

AC XY:

20410

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.221

Gnomad4 ASJ

AF:

0.264

Gnomad4 EAS

AF:

0.0728

Gnomad4 SAS

AF:

0.197

Gnomad4 FIN

AF:

0.288

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.269

Hom.:

13948

Bravo

AF:

0.274

TwinsUK

AF:

0.268

AC:

992

ALSPAC

AF:

0.250

AC:

964

ESP6500AA

AF:

0.350

AC:

1542

ESP6500EA

AF:

0.264

AC:

2271

ExAC

AF:

0.244

AC:

29666

Asia WGS

AF:

0.150

AC:

523

AN:

3478

EpiCase

AF:

0.277

EpiControl

AF:

0.282

ClinVar

Significance: Benign

Submissions summary: Benign:6Other:2

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Immunodeficiency 104

Benign:3

Benign, reviewed by expert panel	curation	ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen	Apr 03, 2024	The c.1066A>G (NM_002185.5) variant in IL7R is a missense variant predicted to cause substitution of Isoleucine by Valine at amino acid 356 (p.Ile356Val). The filtering allele frequency (the lower threshold of the 95% CI of 25619/74900 alleles) of the c.1066A>G variant in IL7R is 0.3385 for African/African American chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (>0.00566) for BA1, and therefore meets this criterion (BA1). Additionally, 55069 adult homozygous occurrences are described in gnomAD (BS2_Supporting). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: BA1 and BS2_Supporting. (VCEP specifications version 1) -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 06, 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 specified

Benign:2Other:1

not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 28, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Benign, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Jan 24, 2024	This variant is classified as Benign based on local population frequency. This variant was detected in 42% of patients studied by a panel of primary immunodeficiencies. Number of patients: 40. Only high quality variants are reported. -

not provided

Benign:1Other:1

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	This variant is associated with the following publications: (PMID: 21297633, 15674389, 24728327, 23818875, 17660816) -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

Cadd

Benign

0.37

Dann

Benign

0.65

DEOGEN2

Benign

0.13

Eigen

Benign

-0.82

Eigen_PC

Benign

-0.84

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.33

MetaRNN

Benign

0.0044

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.6

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.27

PROVEAN

Benign

0.080

REVEL

Benign

0.019

Sift

Benign

0.68

Sift4G

Benign

1.0

Polyphen

0.044

Vest4

0.0060

MPC

0.014

ClinPred

0.0074

GERP RS

3.2

Varity_R

0.031

gMVP

0.12

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over