chr19-1818538-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.2960G>A(p.Arg987His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,611,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 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.2960G>A | p.Arg987His | missense_variant | 10/16 | ENST00000170168.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REXO1 | ENST00000170168.9 | c.2960G>A | p.Arg987His | missense_variant | 10/16 | 1 | NM_020695.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152228Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 247046Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134370
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1459612Hom.: 0 Cov.: 35 AF XY: 0.0000152 AC XY: 11AN XY: 726024
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152228Hom.: 0 Cov.: 34 AF XY: 0.0000941 AC XY: 7AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2023 | The c.2960G>A (p.R987H) alteration is located in exon 10 (coding exon 10) of the REXO1 gene. This alteration results from a G to A substitution at nucleotide position 2960, causing the arginine (R) at amino acid position 987 to be replaced by a histidine (H). 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