5-35876113-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_002185.5(IL7R):āc.1007A>Gā(p.Glu336Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002185.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL7R | NM_002185.5 | c.1007A>G | p.Glu336Gly | missense_variant | Exon 8 of 8 | ENST00000303115.8 | NP_002176.2 | |
IL7R | NM_001410734.1 | c.*124A>G | 3_prime_UTR_variant | Exon 7 of 7 | NP_001397663.1 | |||
IL7R | NR_120485.3 | n.831A>G | non_coding_transcript_exon_variant | Exon 6 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000358 AC: 90AN: 251196Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135744
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461880Hom.: 0 Cov.: 32 AF XY: 0.0000646 AC XY: 47AN XY: 727240
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
Immunodeficiency 104 Uncertain:1Benign:1
IL7R NM_002185.4 exon 8 p.Glu336Gly (c.1007A>G): This variant has not been reported in the literature but is present in 0.2% (95/35406) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/5-35876215-A-G?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:464436). Evolutionary conservation for this variant is unclear; computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at