chr19-1817736-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020695.4(REXO1):c.3061G>A(p.Ala1021Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000614 in 1,612,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REXO1 | NM_020695.4 | c.3061G>A | p.Ala1021Thr | missense_variant | 11/16 | ENST00000170168.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REXO1 | ENST00000170168.9 | c.3061G>A | p.Ala1021Thr | missense_variant | 11/16 | 1 | NM_020695.4 | P2 | |
REXO1 | ENST00000643515.1 | c.988G>A | p.Ala330Thr | missense_variant | 7/12 | A2 | |||
REXO1 | ENST00000588743.2 | n.189G>A | non_coding_transcript_exon_variant | 3/4 | 3 | ||||
REXO1 | ENST00000590936.5 | c.442G>A | p.Ala148Thr | missense_variant, NMD_transcript_variant | 5/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000896 AC: 22AN: 245538Hom.: 0 AF XY: 0.0000897 AC XY: 12AN XY: 133810
GnomAD4 exome AF: 0.0000596 AC: 87AN: 1459938Hom.: 0 Cov.: 32 AF XY: 0.0000688 AC XY: 50AN XY: 726270
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.3061G>A (p.A1021T) alteration is located in exon 11 (coding exon 11) of the REXO1 gene. This alteration results from a G to A substitution at nucleotide position 3061, causing the alanine (A) at amino acid position 1021 to be replaced by a threonine (T). 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