12-102118354-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_024057.4(NUP37):c.156+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000549 in 1,609,328 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00031 ( 3 hom. )
Consequence
NUP37
NM_024057.4 intron
NM_024057.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.329
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 12-102118354-T-C is Benign according to our data. Variant chr12-102118354-T-C is described in ClinVar as [Benign]. Clinvar id is 3038891.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP37 | NM_024057.4 | c.156+9A>G | intron_variant | ENST00000552283.6 | |||
NUP37 | XM_047429530.1 | c.156+9A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP37 | ENST00000552283.6 | c.156+9A>G | intron_variant | 5 | NM_024057.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00285 AC: 434AN: 152230Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000670 AC: 165AN: 246292Hom.: 2 AF XY: 0.000481 AC XY: 64AN XY: 133118
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GnomAD4 exome AF: 0.000308 AC: 449AN: 1456980Hom.: 3 Cov.: 31 AF XY: 0.000264 AC XY: 191AN XY: 724648
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NUP37-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 28, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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