chr7-135570950-A-ATAGT
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_015135.3(NUP205):c.29-153_29-152insGTTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 135,456 control chromosomes in the GnomAD database, including 75 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.025 ( 75 hom., cov: 26)
Consequence
NUP205
NM_015135.3 intron
NM_015135.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.264
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 -10 ACMG points.
BP6
Variant 7-135570950-A-ATAGT is Benign according to our data. Variant chr7-135570950-A-ATAGT is described in ClinVar as [Benign]. Clinvar id is 1226308.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.29-153_29-152insGTTA | intron_variant | ENST00000285968.11 | |||
NUP205 | NM_001329434.2 | c.-1057-153_-1057-152insGTTA | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.29-153_29-152insGTTA | intron_variant | 1 | NM_015135.3 | P1 | |||
NUP205 | ENST00000489493.1 | n.284-153_284-152insGTTA | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0251 AC: 3400AN: 135460Hom.: 75 Cov.: 26
GnomAD3 genomes
AF:
AC:
3400
AN:
135460
Hom.:
Cov.:
26
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0251 AC: 3401AN: 135456Hom.: 75 Cov.: 26 AF XY: 0.0265 AC XY: 1708AN XY: 64388
GnomAD4 genome
AF:
AC:
3401
AN:
135456
Hom.:
Cov.:
26
AF XY:
AC XY:
1708
AN XY:
64388
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 | Dec 08, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at