chr11-47804538-A-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015231.3(NUP160):c.2574+11T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 1,512,470 control chromosomes in the GnomAD database, including 144,843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.35 ( 10568 hom., cov: 33)
Exomes 𝑓: 0.44 ( 134275 hom. )
Consequence
NUP160
NM_015231.3 intron
NM_015231.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.173
Genes affected
NUP160 (HGNC:18017): (nucleoporin 160) A structural constituent of nuclear pore. Involved in mRNA export from nucleus and nephron development. Part of nuclear pore outer ring. Colocalizes with kinetochore. Implicated in nephrotic syndrome type 19. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 11-47804538-A-C is Benign according to our data. Variant chr11-47804538-A-C is described in ClinVar as [Benign]. Clinvar id is 1327015.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP160 | NM_015231.3 | c.2574+11T>G | intron_variant | ENST00000378460.7 | |||
NUP160 | NR_134636.3 | n.2621+11T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP160 | ENST00000378460.7 | c.2574+11T>G | intron_variant | 1 | NM_015231.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.347 AC: 52688AN: 152034Hom.: 10569 Cov.: 33
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GnomAD3 exomes AF: 0.407 AC: 74952AN: 184372Hom.: 16353 AF XY: 0.422 AC XY: 42921AN XY: 101656
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GnomAD4 exome AF: 0.437 AC: 594823AN: 1360318Hom.: 134275 Cov.: 24 AF XY: 0.441 AC XY: 298505AN XY: 676610
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GnomAD4 genome AF: 0.346 AC: 52682AN: 152152Hom.: 10568 Cov.: 33 AF XY: 0.343 AC XY: 25505AN XY: 74392
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Nephrotic syndrome, type 19 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at