rs11567714

chr5-35862883-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002185.5(IL7R):c.221+1893C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 152,158 control chromosomes in the GnomAD database, including 614 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 0.077 (614 hom., cov: 32)
• Consequence: IL7R NM_002185.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL7R	NM_002185.5	c.221+1893C>T		intron_variant		ENST00000303115.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL7R	ENST00000303115.8	c.221+1893C>T		intron_variant		1	NM_002185.5	P1

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11780 AN: 152040 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0556

Gnomad FIN AF: 0.0804

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0774 AC: 11784 AN: 152158 Hom.: 614 Cov.: 32 AF XY: 0.0759 AC XY: 5647 AN XY: 74386

Gnomad4 AFR AF: 0.0207

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.0804

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0896

Alfa AF: 0.0929 Hom.: 173

Bravo AF: 0.0749

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	6.3
Dann	Benign	0.86

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

Other links and lift over

dbSNP: rs11567714; hg19: chr5-35862985;