rs72650663
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM1BP4_StrongBP6_Very_StrongBS2
The NM_022168.4(IFIH1):c.2105C>T(p.Thr702Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00331 in 1,612,420 control chromosomes in the GnomAD database, including 20 homozygotes. 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 (★★).
Frequency
Consequence
NM_022168.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFIH1 | NM_022168.4 | c.2105C>T | p.Thr702Ile | missense_variant | 11/16 | ENST00000649979.2 | NP_071451.2 | |
IFIH1 | XM_047445407.1 | c.1388C>T | p.Thr463Ile | missense_variant | 10/15 | XP_047301363.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFIH1 | ENST00000649979.2 | c.2105C>T | p.Thr702Ile | missense_variant | 11/16 | NM_022168.4 | ENSP00000497271 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00248 AC: 377AN: 152002Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00235 AC: 587AN: 249830Hom.: 0 AF XY: 0.00248 AC XY: 334AN XY: 134912
GnomAD4 exome AF: 0.00340 AC: 4964AN: 1460300Hom.: 18 Cov.: 31 AF XY: 0.00343 AC XY: 2492AN XY: 726402
GnomAD4 genome AF: 0.00248 AC: 377AN: 152120Hom.: 2 Cov.: 32 AF XY: 0.00218 AC XY: 162AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | IFIH1: BP4, BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Aicardi-Goutieres syndrome 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Jun 30, 2020 | - - |
Aicardi-Goutieres syndrome 7;C4225427:Singleton-Merten syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
IFIH1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 25, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at