chr19-1819089-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.2693G>A(p.Gly898Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000325 in 1,598,026 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000030 ( 0 hom. )
Consequence
REXO1
NM_020695.4 missense
NM_020695.4 missense
Scores
1
7
11
Clinical Significance
Conservation
PhyloP100: 6.49
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.17422163).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REXO1 | NM_020695.4 | c.2693G>A | p.Gly898Glu | missense_variant | 8/16 | ENST00000170168.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REXO1 | ENST00000170168.9 | c.2693G>A | p.Gly898Glu | missense_variant | 8/16 | 1 | NM_020695.4 | P2 | |
REXO1 | ENST00000643515.1 | c.620G>A | p.Gly207Glu | missense_variant | 4/12 | A2 | |||
REXO1 | ENST00000590936.5 | c.74G>A | p.Gly25Glu | missense_variant, NMD_transcript_variant | 2/10 | 5 | |||
REXO1 | ENST00000586343.2 | c.*278G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152188Hom.: 1 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000548 AC: 13AN: 237106Hom.: 0 AF XY: 0.0000544 AC XY: 7AN XY: 128678
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GnomAD4 exome AF: 0.0000304 AC: 44AN: 1445720Hom.: 0 Cov.: 33 AF XY: 0.0000334 AC XY: 24AN XY: 717910
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GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152306Hom.: 1 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74478
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2023 | The c.2693G>A (p.G898E) alteration is located in exon 8 (coding exon 8) of the REXO1 gene. This alteration results from a G to A substitution at nucleotide position 2693, causing the glycine (G) at amino acid position 898 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.
REVEL
Benign
Sift
Uncertain
D;.
Sift4G
Uncertain
D;.
Polyphen
D;.
Vest4
MutPred
Gain of solvent accessibility (P = 0.0171);.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at