chr19-1818490-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.3008G>A(p.Arg1003Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00025 in 1,601,520 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 (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00026 ( 0 hom. )
Consequence
REXO1
NM_020695.4 missense
NM_020695.4 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 5.13
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=0.16741082).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REXO1 | NM_020695.4 | c.3008G>A | p.Arg1003Gln | missense_variant | 10/16 | ENST00000170168.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REXO1 | ENST00000170168.9 | c.3008G>A | p.Arg1003Gln | missense_variant | 10/16 | 1 | NM_020695.4 | P2 | |
REXO1 | ENST00000643515.1 | c.935G>A | p.Arg312Gln | missense_variant | 6/12 | A2 | |||
REXO1 | ENST00000588743.2 | n.136G>A | non_coding_transcript_exon_variant | 2/4 | 3 | ||||
REXO1 | ENST00000590936.5 | c.389G>A | p.Arg130Gln | missense_variant, NMD_transcript_variant | 4/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152164Hom.: 0 Cov.: 34
GnomAD3 genomes
?
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34
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GnomAD3 exomes AF: 0.000130 AC: 30AN: 230480Hom.: 0 AF XY: 0.000120 AC XY: 15AN XY: 125292
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GnomAD4 exome AF: 0.000261 AC: 379AN: 1449356Hom.: 0 Cov.: 34 AF XY: 0.000239 AC XY: 172AN XY: 719912
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GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152164Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74326
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ExAC
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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 | Mar 31, 2023 | The c.3008G>A (p.R1003Q) 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 3008, causing the arginine (R) at amino acid position 1003 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
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
Benign
N;.
REVEL
Benign
Sift
Benign
D;.
Sift4G
Benign
T;.
Polyphen
P;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at