1-18910367-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001136265.2(IFFO2):c.1423C>T(p.Arg475Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,612,864 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 Uncertain significance (★).
Frequency
Consequence
NM_001136265.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFFO2 | NM_001136265.2 | c.1423C>T | p.Arg475Trp | missense_variant | Exon 8 of 9 | ENST00000455833.7 | NP_001129737.1 | |
IFFO2 | XM_011540630.3 | c.1282C>T | p.Arg428Trp | missense_variant | Exon 7 of 8 | XP_011538932.1 | ||
IFFO2 | XM_047444839.1 | c.1186C>T | p.Arg396Trp | missense_variant | Exon 6 of 7 | XP_047300795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFFO2 | ENST00000455833.7 | c.1423C>T | p.Arg475Trp | missense_variant | Exon 8 of 9 | 5 | NM_001136265.2 | ENSP00000387941.2 | ||
IFFO2 | ENST00000416166.1 | c.646C>T | p.Arg216Trp | missense_variant | Exon 7 of 8 | 3 | ENSP00000394655.1 | |||
IFFO2 | ENST00000355609.8 | c.136C>T | p.Arg46Trp | missense_variant | Exon 2 of 3 | 5 | ENSP00000347820.4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248620Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134494
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1460634Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 726450
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1423C>T (p.R475W) alteration is located in exon 8 (coding exon 8) of the IFFO2 gene. This alteration results from a C to T substitution at nucleotide position 1423, causing the arginine (R) at amino acid position 475 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at