Variant 5-35875491-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002185.5(IL7R):c.801-21A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 1,562,986 control chromosomes in the GnomAD database, including 215,222 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 21185 hom., cov: 32)

Exomes 𝑓: 0.52 ( 194037 hom. )

Consequence

IL7R
NM_002185.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.139

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 (BayesDel_noAF=-0.87).

BP6

Variant 5-35875491-A-T is Benign according to our data. Variant chr5-35875491-A-T is described in ClinVar as [Benign]. Clinvar id is 1165796.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-35875491-A-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL7R	NM_002185.5 linkuse as main transcript	c.801-21A>T		intron_variant		ENST00000303115.8	NP_002176.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL7R	ENST00000303115.8 linkuse as main transcript	c.801-21A>T		intron_variant		1	NM_002185.5	ENSP00000306157	P1	P16871-1

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79445

AN:

151860

Hom.:

21184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.556

Gnomad AMI

AF:

0.650

Gnomad AMR

AF:

0.412

Gnomad ASJ

AF:

0.507

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.447

Gnomad FIN

AF:

0.635

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.535

Gnomad OTH

AF:

0.489

GnomAD3 exomes

AF:

0.488

AC:

121833

AN:

249882

Hom.:

31117

AF XY:

0.494

AC XY:

66710

AN XY:

134982

show subpopulations

Gnomad AFR exome

AF:

0.562

Gnomad AMR exome

AF:

0.334

Gnomad ASJ exome

AF:

0.502

Gnomad EAS exome

AF:

0.271

Gnomad SAS exome

AF:

0.457

Gnomad FIN exome

AF:

0.632

Gnomad NFE exome

AF:

0.537

Gnomad OTH exome

AF:

0.514

GnomAD4 exome

AF:

0.520

AC:

734085

AN:

1411008

Hom.:

194037

Cov.:

AF XY:

0.519

AC XY:

366303

AN XY:

705146

show subpopulations

Gnomad4 AFR exome

AF:

0.560

Gnomad4 AMR exome

AF:

0.349

Gnomad4 ASJ exome

AF:

0.510

Gnomad4 EAS exome

AF:

0.290

Gnomad4 SAS exome

AF:

0.456

Gnomad4 FIN exome

AF:

0.631

Gnomad4 NFE exome

AF:

0.536

Gnomad4 OTH exome

AF:

0.506

GnomAD4 genome

AF:

0.523

AC:

79473

AN:

151978

Hom.:

21185

Cov.:

AF XY:

0.523

AC XY:

38851

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.556

Gnomad4 AMR

AF:

0.412

Gnomad4 ASJ

AF:

0.507

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.446

Gnomad4 FIN

AF:

0.635

Gnomad4 NFE

AF:

0.535

Gnomad4 OTH

AF:

0.487

Alfa

AF:

0.530

Hom.:

3949

Bravo

AF:

0.506

Asia WGS

AF:

0.412

AC:

1432

AN:

3478

EpiCase

AF:

0.526

EpiControl

AF:

0.537

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	This variant is associated with the following publications: (PMID: 19523791, 17660816, 15674389) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Immunodeficiency 104

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 19, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 19, 2024	- -

not specified

Benign:1

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 63% of patients studied by a panel of primary immunodeficiencies. Number of patients: 60. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.081

DANN

Benign

0.40

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