rs8051691
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_014669.5(NUP93):c.360+3262G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000013 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
NUP93
NM_014669.5 intron
NM_014669.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.555
Genes affected
NUP93 (HGNC:28958): (nucleoporin 93) The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. This gene encodes a nucleoporin protein that localizes both to the basket of the pore and to the nuclear entry of the central gated channel of the pore. The encoded protein is a target of caspase cysteine proteases that play a central role in programmed cell death by apoptosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUP93 | NM_014669.5 | c.360+3262G>A | intron_variant | ENST00000308159.10 | NP_055484.3 | |||
NUP93 | NM_001242795.2 | c.-10+3262G>A | intron_variant | NP_001229724.1 | ||||
NUP93 | NM_001242796.2 | c.-10+3262G>A | intron_variant | NP_001229725.1 | ||||
NUP93 | XM_005256263.4 | c.360+3262G>A | intron_variant | XP_005256320.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUP93 | ENST00000308159.10 | c.360+3262G>A | intron_variant | 1 | NM_014669.5 | ENSP00000310668.5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151960Hom.: 0 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000132 AC: 2AN: 151960Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74214
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
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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