19-1816091-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020695.4(REXO1):c.3641G>A(p.Arg1214Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000226 in 1,547,772 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020695.4 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 |
---|---|---|---|---|---|---|---|
REXO1 | NM_020695.4 | c.3641G>A | p.Arg1214Gln | missense_variant | 16/16 | ENST00000170168.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REXO1 | ENST00000170168.9 | c.3641G>A | p.Arg1214Gln | missense_variant | 16/16 | 1 | NM_020695.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000195 AC: 3AN: 154170Hom.: 0 AF XY: 0.0000246 AC XY: 2AN XY: 81364
GnomAD4 exome AF: 0.0000215 AC: 30AN: 1395510Hom.: 1 Cov.: 39 AF XY: 0.0000189 AC XY: 13AN XY: 688504
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2023 | The c.3641G>A (p.R1214Q) alteration is located in exon 16 (coding exon 16) of the REXO1 gene. This alteration results from a G to A substitution at nucleotide position 3641, causing the arginine (R) at amino acid position 1214 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