7-135570871-A-ATATATGTAATATATTATATATTATATATT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_015135.3(NUP205):c.29-228_29-200dupGTAATATATTATATATTATATATTTATAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0856 in 102,606 control chromosomes in the GnomAD database, including 1,222 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.086 ( 1222 hom., cov: 21)
Consequence
NUP205
NM_015135.3 intron
NM_015135.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
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 7-135570871-A-ATATATGTAATATATTATATATTATATATT is Benign according to our data. Variant chr7-135570871-A-ATATATGTAATATATTATATATTATATATT is described in ClinVar as [Benign]. Clinvar id is 1245148.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.29-228_29-200dupGTAATATATTATATATTATATATTTATAT | intron_variant | Intron 1 of 42 | ENST00000285968.11 | NP_055950.2 | ||
NUP205 | NM_001329434.2 | c.-1057-228_-1057-200dupGTAATATATTATATATTATATATTTATAT | intron_variant | Intron 1 of 42 | NP_001316363.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.29-234_29-233insTATATGTAATATATTATATATTATATATT | intron_variant | Intron 1 of 42 | 1 | NM_015135.3 | ENSP00000285968.6 | |||
NUP205 | ENST00000489493.1 | n.284-234_284-233insTATATGTAATATATTATATATTATATATT | intron_variant | Intron 1 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0856 AC: 8785AN: 102600Hom.: 1221 Cov.: 21
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GnomAD4 genome AF: 0.0856 AC: 8783AN: 102606Hom.: 1222 Cov.: 21 AF XY: 0.0772 AC XY: 3597AN XY: 46566
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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
Dec 18, 2019
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at