13-20799320-A-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_022459.5(XPO4):c.2167T>A(p.Cys723Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022459.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XPO4 | NM_022459.5 | c.2167T>A | p.Cys723Ser | missense_variant | 16/23 | ENST00000255305.11 | NP_071904.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XPO4 | ENST00000255305.11 | c.2167T>A | p.Cys723Ser | missense_variant | 16/23 | 1 | NM_022459.5 | ENSP00000255305.6 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249218Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135220
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461310Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726942
GnomAD4 genome AF: 0.000151 AC: 23AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 20, 2024 | The c.2167T>A (p.C723S) alteration is located in exon 16 (coding exon 16) of the XPO4 gene. This alteration results from a T to A substitution at nucleotide position 2167, causing the cysteine (C) at amino acid position 723 to be replaced by a serine (S). 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