21-33241958-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001289125.3(IFNAR2):c.36A>G(p.Ser12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,460,548 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. S12S) has been classified as Likely benign.
Frequency
Consequence
NM_001289125.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNAR2 | NM_001289125.3 | c.36A>G | p.Ser12= | synonymous_variant | 2/9 | ENST00000342136.9 | |
IFNAR2-IL10RB | NM_001414505.1 | c.36A>G | p.Ser12= | synonymous_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNAR2 | ENST00000342136.9 | c.36A>G | p.Ser12= | synonymous_variant | 2/9 | 1 | NM_001289125.3 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250106Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135218
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460548Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726596
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at