chr7-135571279-AT-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_015135.3(NUP205):c.171+45del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 953,788 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 28)
Exomes 𝑓: 0.19 ( 0 hom. )
Consequence
NUP205
NM_015135.3 intron
NM_015135.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.58
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 -10 ACMG points.
BP6
Variant 7-135571279-AT-A is Benign according to our data. Variant chr7-135571279-AT-A is described in ClinVar as [Benign]. Clinvar id is 1280600.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.171+45del | intron_variant | ENST00000285968.11 | |||
NUP205 | NM_001329434.2 | c.-915+45del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.171+45del | intron_variant | 1 | NM_015135.3 | P1 | |||
NUP205 | ENST00000489493.1 | n.426+45del | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00129 AC: 178AN: 138292Hom.: 0 Cov.: 28
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GnomAD3 exomes AF: 0.310 AC: 18179AN: 58698Hom.: 0 AF XY: 0.324 AC XY: 10520AN XY: 32468
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GnomAD4 exome AF: 0.185 AC: 150948AN: 815478Hom.: 0 Cov.: 0 AF XY: 0.189 AC XY: 74835AN XY: 395524
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GnomAD4 genome AF: 0.00129 AC: 179AN: 138310Hom.: 0 Cov.: 28 AF XY: 0.00161 AC XY: 108AN XY: 66946
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2020 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at