Genetic Variant NUP205:c.29-200_29-199insGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATTTATAT (chr7-135570871-A-ATATATGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015135.3(NUP205):c.29-200_29-199insGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATTTATAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000172 in 104,612 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00017 ( 0 hom., cov: 21)

Consequence

NUP205
NM_015135.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

0 publications found

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]

NUP205 Gene-Disease associations (from GenCC):

nephrotic syndrome, type 13
Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae)
familial idiopathic steroid-resistant nephrotic syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

NUP205 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015135.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP205	NM_015135.3	MANE Select	c.29-200_29-199insGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATTTATAT		intron	N/A	NP_055950.2	Q92621
	NUP205	NM_001329434.2		c.-1057-200_-1057-199insGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATTTATAT		intron	N/A	NP_001316363.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NUP205	ENST00000285968.11	TSL:1 MANE Select	c.29-234_29-233insTATATGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATT	intron	N/A	ENSP00000285968.6	Q92621
NUP205	ENST00000921555.1		c.125-234_125-233insTATATGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATT	intron	N/A	ENSP00000591614.1
NUP205	ENST00000921547.1		c.29-234_29-233insTATATGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATT	intron	N/A	ENSP00000591606.1

Frequencies

GnomAD3 genomes

AF:

0.000172

AC:

AN:

104604

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000358

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000130

Gnomad ASJ

AF:

0.00341

Gnomad EAS

AF:

0.000727

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000374

Gnomad OTH

AF:

0.000776

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.000172

AC:

AN:

104612

Hom.:

Cov.:

AF XY:

0.000127

AC XY:

AN XY:

47346

show subpopulations

African (AFR)

AF:

0.0000357

AC:

AN:

27982

American (AMR)

AF:

0.000130

AC:

AN:

7718

Ashkenazi Jewish (ASJ)

AF:

0.00341

AC:

AN:

2936

East Asian (EAS)

AF:

0.000730

AC:

AN:

4110

South Asian (SAS)

AF:

0.00

AC:

AN:

3672

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2588

Middle Eastern (MID)

AF:

0.00

AC:

AN:

224

European-Non Finnish (NFE)

AF:

0.0000374

AC:

AN:

53470

Other (OTH)

AF:

0.000770

AC:

AN:

1298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.544

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.0

Splicing

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

Publications

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7-135570871-ATATATGTAATATATTATATATTATATATT-ATATATGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATTTATATGTAATATATTATATATTATATATT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over