7-135570871-A-ATATATGTAATATATTATATATTATATATT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015135.3(NUP205):​c.29-228_29-200dupGTAATATATTATATATTATATATTTATAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0856 in 102,606 control chromosomes in the GnomAD database, including 1,222 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.086 ( 1222 hom., cov: 21)

Consequence

NUP205
NM_015135.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00
Variant links:
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 7-135570871-A-ATATATGTAATATATTATATATTATATATT is Benign according to our data. Variant chr7-135570871-A-ATATATGTAATATATTATATATTATATATT is described in ClinVar as [Benign]. Clinvar id is 1245148.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NUP205NM_015135.3 linkc.29-228_29-200dupGTAATATATTATATATTATATATTTATAT intron_variant Intron 1 of 42 ENST00000285968.11 NP_055950.2 Q92621
NUP205NM_001329434.2 linkc.-1057-228_-1057-200dupGTAATATATTATATATTATATATTTATAT intron_variant Intron 1 of 42 NP_001316363.2 Q92621

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NUP205ENST00000285968.11 linkc.29-234_29-233insTATATGTAATATATTATATATTATATATT intron_variant Intron 1 of 42 1 NM_015135.3 ENSP00000285968.6 Q92621
NUP205ENST00000489493.1 linkn.284-234_284-233insTATATGTAATATATTATATATTATATATT intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.0856
AC:
8785
AN:
102600
Hom.:
1221
Cov.:
21
show subpopulations
Gnomad AFR
AF:
0.0303
Gnomad AMI
AF:
0.202
Gnomad AMR
AF:
0.0662
Gnomad ASJ
AF:
0.0717
Gnomad EAS
AF:
0.161
Gnomad SAS
AF:
0.0866
Gnomad FIN
AF:
0.0452
Gnomad MID
AF:
0.0336
Gnomad NFE
AF:
0.114
Gnomad OTH
AF:
0.0678
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0856
AC:
8783
AN:
102606
Hom.:
1222
Cov.:
21
AF XY:
0.0772
AC XY:
3597
AN XY:
46566
show subpopulations
Gnomad4 AFR
AF:
0.0303
Gnomad4 AMR
AF:
0.0662
Gnomad4 ASJ
AF:
0.0717
Gnomad4 EAS
AF:
0.162
Gnomad4 SAS
AF:
0.0863
Gnomad4 FIN
AF:
0.0452
Gnomad4 NFE
AF:
0.114
Gnomad4 OTH
AF:
0.0673

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 18, 2019
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1491577075; hg19: chr7-135255619; API