chr9-133412319-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020385.4(REXO4):c.890G>A(p.Arg297Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000251 in 1,613,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. R297W) has been classified as Uncertain significance.
Frequency
Consequence
NM_020385.4 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 |
---|---|---|---|---|---|---|---|
REXO4 | NM_020385.4 | c.890G>A | p.Arg297Gln | missense_variant | 4/8 | ENST00000371942.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REXO4 | ENST00000371942.8 | c.890G>A | p.Arg297Gln | missense_variant | 4/8 | 1 | NM_020385.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000267 AC: 67AN: 251276Hom.: 0 AF XY: 0.000272 AC XY: 37AN XY: 135784
GnomAD4 exome AF: 0.000263 AC: 384AN: 1461654Hom.: 0 Cov.: 30 AF XY: 0.000246 AC XY: 179AN XY: 727150
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.890G>A (p.R297Q) alteration is located in exon 4 (coding exon 4) of the REXO4 gene. This alteration results from a G to A substitution at nucleotide position 890, causing the arginine (R) at amino acid position 297 to be replaced by a glutamine (Q). 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