chr21-33403590-TCGC-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM2PM4_SupportingBP6BS1
The NM_005534.4(IFNGR2):c.60_62delCGC(p.Ala21del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000703 in 1,211,410 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_005534.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 150188Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00347 AC: 175AN: 50422Hom.: 0 AF XY: 0.00313 AC XY: 94AN XY: 30078
GnomAD4 exome AF: 0.000703 AC: 852AN: 1211410Hom.: 0 AF XY: 0.000812 AC XY: 482AN XY: 593408
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000666 AC: 1AN: 150188Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73310
ClinVar
Submissions by phenotype
IFNGR2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at