chr7-135557940-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_015135.3(NUP205):c.-5C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,613,584 control chromosomes in the GnomAD database, including 140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0028 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0036 ( 131 hom. )
Consequence
NUP205
NM_015135.3 5_prime_UTR
NM_015135.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.424
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 7-135557940-C-T is Benign according to our data. Variant chr7-135557940-C-T is described in ClinVar as [Benign]. Clinvar id is 1266093.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0561 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.-5C>T | 5_prime_UTR_variant | 1/43 | ENST00000285968.11 | ||
NUP205 | NM_001329434.2 | c.-1090C>T | 5_prime_UTR_variant | 1/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.-5C>T | 5_prime_UTR_variant | 1/43 | 1 | NM_015135.3 | P1 | ||
NUP205 | ENST00000489493.1 | n.9C>T | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00281 AC: 427AN: 152196Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00808 AC: 2033AN: 251462Hom.: 50 AF XY: 0.00912 AC XY: 1239AN XY: 135904
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GnomAD4 exome AF: 0.00361 AC: 5268AN: 1461270Hom.: 131 Cov.: 29 AF XY: 0.00439 AC XY: 3193AN XY: 726996
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GnomAD4 genome AF: 0.00279 AC: 425AN: 152314Hom.: 9 Cov.: 32 AF XY: 0.00341 AC XY: 254AN XY: 74472
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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 28, 2020 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at