chr21-33403552-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_005534.4(IFNGR2):c.9G>A(p.Pro3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000679 in 1,177,596 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P3P) has been classified as Likely benign.
Frequency
Consequence
NM_005534.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNGR2 | NM_005534.4 | c.9G>A | p.Pro3= | synonymous_variant | 1/7 | ENST00000290219.11 | |
IFNGR2 | NM_001329128.2 | c.9G>A | p.Pro3= | synonymous_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNGR2 | ENST00000290219.11 | c.9G>A | p.Pro3= | synonymous_variant | 1/7 | 1 | NM_005534.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000169 AC: 1AN: 59132Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 35196
GnomAD4 exome AF: 0.00000679 AC: 8AN: 1177596Hom.: 0 Cov.: 31 AF XY: 0.00000868 AC XY: 5AN XY: 576216
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Immunodeficiency 28 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at