rs11567685

Variant names:

• chr5-35856473-T-C
• rs11567685
• ENST00000515665:c.-216T>C

Variant summary

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

The ENST00000515665(IL7R):​c.-216T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 157,252 control chromosomes in the GnomAD database, including 5,480 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 0.26 (5364 hom., cov: 33)
  • Exomes 𝑓: 0.19 (116 hom.)
• Consequence: IL7R ENST00000515665 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL7R	ENST00000515665	c.-216T>C		5_prime_UTR_variant	Exon 1 of 3	4		ENSP00000425538.1
IL7R	ENST00000508941.5	c.-2+304T>C		intron_variant	Intron 2 of 3	4		ENSP00000426426.1
IL7R	ENST00000511031.1	n.216+3535T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39361 AN: 152014 Hom.: 5361 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0447

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.267

GnomAD4 exome AF: 0.187 AC: 959 AN: 5120 Hom.: 116 Cov.: 0 AF XY: 0.185 AC XY: 497 AN XY: 2686

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.157

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.0288

Gnomad4 SAS exome AF: 0.140

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.213

Gnomad4 OTH exome AF: 0.202

GnomAD4 genome AF: 0.259 AC: 39361 AN: 152132 Hom.: 5364 Cov.: 33 AF XY: 0.257 AC XY: 19106 AN XY: 74354

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.0448

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.263

Alfa AF: 0.267 Hom.: 8703

Bravo AF: 0.253

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11567685; hg19: chr5-35856575;