rs2257167
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000629.3(IFNAR1):c.502G>C(p.Val168Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,610,902 control chromosomes in the GnomAD database, including 21,248 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. V168V) has been classified as Benign.
Frequency
Consequence
NM_000629.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNAR1 | NM_000629.3 | c.502G>C | p.Val168Leu | missense_variant | 4/11 | ENST00000270139.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNAR1 | ENST00000270139.8 | c.502G>C | p.Val168Leu | missense_variant | 4/11 | 1 | NM_000629.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.163 AC: 24799AN: 152018Hom.: 2322 Cov.: 33
GnomAD3 exomes AF: 0.185 AC: 46302AN: 250954Hom.: 5194 AF XY: 0.186 AC XY: 25166AN XY: 135658
GnomAD4 exome AF: 0.150 AC: 218622AN: 1458768Hom.: 18918 Cov.: 30 AF XY: 0.153 AC XY: 111246AN XY: 725878
GnomAD4 genome ? AF: 0.163 AC: 24812AN: 152134Hom.: 2330 Cov.: 33 AF XY: 0.165 AC XY: 12282AN XY: 74386
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 40% of patients studied by a panel of primary immunodeficiencies. Number of patients: 38. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at