chr7-135571078-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015135.3(NUP205):c.29-27G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0177 in 1,522,034 control chromosomes in the GnomAD database, including 474 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.025 ( 79 hom., cov: 28)
Exomes 𝑓: 0.017 ( 395 hom. )
Consequence
NUP205
NM_015135.3 intron
NM_015135.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.357
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 7-135571078-G-A is Benign according to our data. Variant chr7-135571078-G-A is described in ClinVar as [Benign]. Clinvar id is 1262162.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0705 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.29-27G>A | intron_variant | ENST00000285968.11 | |||
NUP205 | NM_001329434.2 | c.-1057-27G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.29-27G>A | intron_variant | 1 | NM_015135.3 | P1 | |||
NUP205 | ENST00000489493.1 | n.284-27G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0250 AC: 3707AN: 148110Hom.: 79 Cov.: 28
GnomAD3 genomes
AF:
AC:
3707
AN:
148110
Hom.:
Cov.:
28
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0189 AC: 3934AN: 207784Hom.: 114 AF XY: 0.0209 AC XY: 2387AN XY: 114404
GnomAD3 exomes
AF:
AC:
3934
AN:
207784
Hom.:
AF XY:
AC XY:
2387
AN XY:
114404
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0169 AC: 23210AN: 1373836Hom.: 395 Cov.: 28 AF XY: 0.0180 AC XY: 12316AN XY: 683584
GnomAD4 exome
AF:
AC:
23210
AN:
1373836
Hom.:
Cov.:
28
AF XY:
AC XY:
12316
AN XY:
683584
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0251 AC: 3714AN: 148198Hom.: 79 Cov.: 28 AF XY: 0.0261 AC XY: 1880AN XY: 72150
GnomAD4 genome
AF:
AC:
3714
AN:
148198
Hom.:
Cov.:
28
AF XY:
AC XY:
1880
AN XY:
72150
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
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
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at