chr7-135557999-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015135.3(NUP205):c.28+27T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.02 in 1,601,062 control chromosomes in the GnomAD database, including 400 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.016 ( 28 hom., cov: 32)
Exomes 𝑓: 0.020 ( 372 hom. )
Consequence
NUP205
NM_015135.3 intron
NM_015135.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.184
Genes affected
NUP205 (HGNC:18658): (nucleoporin 205) This gene encodes a nucleoporin, which is a subunit of the nuclear pore complex that functions in active transport of proteins, RNAs and ribonucleoprotein particles between the nucleus and cytoplasm. Mutations in this gene are associated with steroid-resistant nephrotic syndrome. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 7-135557999-T-C is Benign according to our data. Variant chr7-135557999-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1316447.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0158 (2409/152268) while in subpopulation NFE AF= 0.0235 (1596/68012). AF 95% confidence interval is 0.0225. There are 28 homozygotes in gnomad4. There are 1111 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 28 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.28+27T>C | intron_variant | ENST00000285968.11 | |||
NUP205 | NM_001329434.2 | c.-1058+27T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.28+27T>C | intron_variant | 1 | NM_015135.3 | P1 | |||
NUP205 | ENST00000489493.1 | n.68T>C | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0158 AC: 2409AN: 152150Hom.: 28 Cov.: 32
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GnomAD3 exomes AF: 0.0172 AC: 4330AN: 251424Hom.: 51 AF XY: 0.0170 AC XY: 2313AN XY: 135880
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GnomAD4 exome AF: 0.0205 AC: 29655AN: 1448794Hom.: 372 Cov.: 27 AF XY: 0.0198 AC XY: 14308AN XY: 721656
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 29, 2019 | - - |
Computational scores
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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