chr2-162277573-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3BP6
The NM_022168.4(IFIH1):āc.1886T>Cā(p.Phe629Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,610,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F629L) has been classified as Uncertain significance.
Frequency
Consequence
NM_022168.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFIH1 | NM_022168.4 | c.1886T>C | p.Phe629Ser | missense_variant | 10/16 | ENST00000649979.2 | |
IFIH1 | XM_047445407.1 | c.1169T>C | p.Phe390Ser | missense_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFIH1 | ENST00000649979.2 | c.1886T>C | p.Phe629Ser | missense_variant | 10/16 | NM_022168.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250840Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135580
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1458696Hom.: 0 Cov.: 29 AF XY: 0.0000400 AC XY: 29AN XY: 725886
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 07, 2022 | The c.1886T>C (p.F629S) alteration is located in exon 10 (coding exon 10) of the IFIH1 gene. This alteration results from a T to C substitution at nucleotide position 1886, causing the phenylalanine (F) at amino acid position 629 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Aicardi-Goutieres syndrome 7;C4225427:Singleton-Merten syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at