rs3816786
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015024.5(XPO7):c.2944-305T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 216,744 control chromosomes in the GnomAD database, including 15,522 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 0.36 ( 10348 hom., cov: 32)
Exomes 𝑓: 0.38 ( 5174 hom. )
Consequence
XPO7
NM_015024.5 intron
NM_015024.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.433
Genes affected
XPO7 (HGNC:14108): (exportin 7) The transport of protein and large RNAs through the nuclear pore complexes (NPC) is an energy-dependent and regulated process. The import of proteins with a nuclear localization signal (NLS) is accomplished by recognition of one or more clusters of basic amino acids by the importin-alpha/beta complex; see MIM 600685 and MIM 602738. The small GTPase RAN (MIM 601179) plays a key role in NLS-dependent protein import. RAN-binding protein-16 is a member of the importin-beta superfamily of nuclear transport receptors.[supplied by OMIM, Jul 2002]
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPO7 | NM_015024.5 | c.2944-305T>A | intron_variant | ENST00000252512.14 | |||
XPO7 | NM_001100161.2 | c.2971-305T>A | intron_variant | ||||
XPO7 | NM_001362802.2 | c.2878-305T>A | intron_variant | ||||
XPO7 | NR_156173.2 | n.3164-305T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPO7 | ENST00000252512.14 | c.2944-305T>A | intron_variant | 1 | NM_015024.5 | P1 | |||
XPO7 | ENST00000433566.8 | c.2947-305T>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.360 AC: 54667AN: 151904Hom.: 10350 Cov.: 32
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GnomAD4 exome AF: 0.384 AC: 24874AN: 64720Hom.: 5174 AF XY: 0.370 AC XY: 12570AN XY: 33946
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GnomAD4 genome ? AF: 0.360 AC: 54691AN: 152024Hom.: 10348 Cov.: 32 AF XY: 0.356 AC XY: 26452AN XY: 74318
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at