rs10507140
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024057.4(NUP37):c.541-1479G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 207,800 control chromosomes in the GnomAD database, including 542 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 0.035 ( 386 hom., cov: 32)
Exomes 𝑓: 0.038 ( 156 hom. )
Consequence
NUP37
NM_024057.4 intron
NM_024057.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.217
Genes affected
NUP37 (HGNC:29929): (nucleoporin 37) Nuclear pore complexes (NPCs) are used for transporting macromolecules between the cytoplasm and the nucleus. NPCs consist of multiple copies of 30 distinct proteins (nucleoporins), which assemble into biochemically-separable subcomplexes. The protein encoded by this gene is part of a subcomplex (Nup107-160) that is required for proper NPC function as well as for normal kinetochore-microtubule interaction and mitosis. [provided by RefSeq, Dec 2015]
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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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP37 | NM_024057.4 | c.541-1479G>C | intron_variant | ENST00000552283.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP37 | ENST00000552283.6 | c.541-1479G>C | intron_variant | 5 | NM_024057.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0354 AC: 5384AN: 152104Hom.: 382 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.0381 AC: 2116AN: 55578Hom.: 156 AF XY: 0.0393 AC XY: 1171AN XY: 29780
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GnomAD4 genome ? AF: 0.0354 AC: 5396AN: 152222Hom.: 386 Cov.: 32 AF XY: 0.0407 AC XY: 3028AN XY: 74422
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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