chr16-27429962-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_181078.3(IL21R):c.-16-94A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 1,047,690 control chromosomes in the GnomAD database, including 333,930 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_181078.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL21R | ENST00000337929.8 | c.-16-94A>G | intron_variant | Intron 1 of 8 | 1 | NM_181078.3 | ENSP00000338010.3 | |||
IL21R | ENST00000395754.4 | c.-16-94A>G | intron_variant | Intron 1 of 8 | 1 | ENSP00000379103.4 | ||||
IL21R | ENST00000564089.5 | c.-16-94A>G | intron_variant | Intron 2 of 9 | 5 | ENSP00000456707.1 |
Frequencies
GnomAD3 genomes AF: 0.791 AC: 120073AN: 151852Hom.: 47743 Cov.: 29
GnomAD4 exome AF: 0.796 AC: 713142AN: 895720Hom.: 286145 AF XY: 0.801 AC XY: 364650AN XY: 455432
GnomAD4 genome AF: 0.791 AC: 120173AN: 151970Hom.: 47785 Cov.: 29 AF XY: 0.799 AC XY: 59367AN XY: 74292
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 94% of patients studied by a panel of primary immunodeficiencies. Number of patients: 83. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at