rs11125883
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003400.4(XPO1):c.2678-347T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 209,252 control chromosomes in the GnomAD database, including 11,770 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 8184 hom., cov: 31)
Exomes 𝑓: 0.34 ( 3586 hom. )
Consequence
XPO1
NM_003400.4 intron
NM_003400.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.458
Genes affected
XPO1 (HGNC:12825): (exportin 1) This cell-cycle-regulated gene encodes a protein that mediates leucine-rich nuclear export signal (NES)-dependent protein transport. The protein specifically inhibits the nuclear export of Rev and U snRNAs. It is involved in the control of several cellular processes by controlling the localization of cyclin B, MPAK, and MAPKAP kinase 2. This protein also regulates NFAT and AP-1. [provided by RefSeq, Jan 2015]
USP34-DT (HGNC:55262): (USP34 divergent transcript)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPO1 | NM_003400.4 | c.2678-347T>G | intron_variant | ENST00000401558.7 | |||
LOC124907772 | XR_007086332.1 | n.204-468A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPO1 | ENST00000401558.7 | c.2678-347T>G | intron_variant | 1 | NM_003400.4 | P1 | |||
USP34-DT | ENST00000692738.1 | n.549-468A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.310 AC: 47128AN: 151814Hom.: 8181 Cov.: 31
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GnomAD4 exome AF: 0.340 AC: 19499AN: 57320Hom.: 3586 Cov.: 0 AF XY: 0.330 AC XY: 9641AN XY: 29254
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GnomAD4 genome ? AF: 0.310 AC: 47142AN: 151932Hom.: 8184 Cov.: 31 AF XY: 0.315 AC XY: 23391AN XY: 74230
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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