chr7-135571298-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015135.3(NUP205):c.171+51C>T 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 1,174,900 control chromosomes in the GnomAD database, including 552 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.028 ( 94 hom., cov: 29)
Exomes 𝑓: 0.019 ( 458 hom. )
Consequence
NUP205
NM_015135.3 intron
NM_015135.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0430
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=-0.96).
BP6
Variant 7-135571298-C-T is Benign according to our data. Variant chr7-135571298-C-T is described in ClinVar as [Benign]. Clinvar id is 1241367.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.171+51C>T | intron_variant | ENST00000285968.11 | |||
NUP205 | NM_001329434.2 | c.-915+51C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.171+51C>T | intron_variant | 1 | NM_015135.3 | P1 | |||
NUP205 | ENST00000489493.1 | n.426+51C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0280 AC: 4028AN: 143676Hom.: 94 Cov.: 29
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GnomAD3 exomes AF: 0.0219 AC: 2699AN: 123436Hom.: 96 AF XY: 0.0227 AC XY: 1551AN XY: 68188
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GnomAD4 exome AF: 0.0189 AC: 19491AN: 1031160Hom.: 458 Cov.: 15 AF XY: 0.0194 AC XY: 9846AN XY: 506494
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GnomAD4 genome AF: 0.0280 AC: 4027AN: 143740Hom.: 94 Cov.: 29 AF XY: 0.0297 AC XY: 2065AN XY: 69508
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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 | Feb 03, 2020 | - - |
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