chrX-48478516-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012280.4(FTSJ1):c.189C>G(p.Ile63Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,207,420 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I63V) has been classified as Uncertain significance.
Frequency
Consequence
NM_012280.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
FTSJ1 | NM_012280.4 | c.189C>G | p.Ile63Met | missense_variant, splice_region_variant | 3/13 | ENST00000348411.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTSJ1 | ENST00000348411.3 | c.189C>G | p.Ile63Met | missense_variant, splice_region_variant | 3/13 | 1 | NM_012280.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000895 AC: 1AN: 111706Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33906
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181607Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66973
GnomAD4 exome AF: 0.00000274 AC: 3AN: 1095714Hom.: 0 Cov.: 30 AF XY: 0.00000277 AC XY: 1AN XY: 361274
GnomAD4 genome ? AF: 0.00000895 AC: 1AN: 111706Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33906
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 17, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at