chr7-135557955-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_015135.3(NUP205):c.11C>T(p.Pro4Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00626 in 1,613,878 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0052 ( 7 hom., cov: 32)
Exomes 𝑓: 0.0064 ( 39 hom. )
Consequence
NUP205
NM_015135.3 missense
NM_015135.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.828
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 -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0038821697).
BP6
?
Variant 7-135557955-C-T is Benign according to our data. Variant chr7-135557955-C-T is described in ClinVar as [Benign]. Clinvar id is 1619681.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High Homozygotes in GnomAd at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.11C>T | p.Pro4Leu | missense_variant | 1/43 | ENST00000285968.11 | |
NUP205 | NM_001329434.2 | c.-1075C>T | 5_prime_UTR_variant | 1/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.11C>T | p.Pro4Leu | missense_variant | 1/43 | 1 | NM_015135.3 | P1 | |
NUP205 | ENST00000489493.1 | n.24C>T | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00516 AC: 786AN: 152212Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00567 AC: 1427AN: 251458Hom.: 15 AF XY: 0.00595 AC XY: 809AN XY: 135902
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GnomAD4 exome AF: 0.00638 AC: 9325AN: 1461548Hom.: 39 Cov.: 29 AF XY: 0.00646 AC XY: 4697AN XY: 727102
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GnomAD4 genome ? AF: 0.00515 AC: 785AN: 152330Hom.: 7 Cov.: 32 AF XY: 0.00554 AC XY: 413AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
NUP205-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 15, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at