chr2-162277463-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_022168.4(IFIH1):c.1996C>A(p.Pro666Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,608,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P666S) has been classified as Likely benign.
Frequency
Consequence
NM_022168.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFIH1 | NM_022168.4 | c.1996C>A | p.Pro666Thr | missense_variant | 10/16 | ENST00000649979.2 | |
IFIH1 | XM_047445407.1 | c.1279C>A | p.Pro427Thr | missense_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFIH1 | ENST00000649979.2 | c.1996C>A | p.Pro666Thr | missense_variant | 10/16 | NM_022168.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152002Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000246 AC: 6AN: 244328Hom.: 0 AF XY: 0.0000227 AC XY: 3AN XY: 132060
GnomAD4 exome AF: 0.0000247 AC: 36AN: 1456498Hom.: 0 Cov.: 29 AF XY: 0.0000290 AC XY: 21AN XY: 724458
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74226
ClinVar
Submissions by phenotype
Aicardi-Goutieres syndrome 7;C4225427:Singleton-Merten syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at