rs201427795

Variant names:

• chr7-135570950-A-ATAGT
• rs201427795
• NM_015135.3:c.29-153_29-152insGTTA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.264
• Publications: 0 publications found

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

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

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.29-153_29-152insGTTA		intron	N/A	NP_055950.2	Q92621
	NUP205	NM_001329434.2		c.-1057-153_-1057-152insGTTA		intron	N/A	NP_001316363.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP205	ENST00000285968.11	TSL:1 MANE Select	c.29-155_29-154insTAGT		intron	N/A	ENSP00000285968.6	Q92621
	NUP205	ENST00000921555.1		c.125-155_125-154insTAGT		intron	N/A	ENSP00000591614.1
	NUP205	ENST00000921547.1		c.29-155_29-154insTAGT		intron	N/A	ENSP00000591606.1

Frequencies

GnomAD3 genomes AF: 0.0251 AC: 3400 AN: 135460 Hom.: 75 Cov.: 26

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.0244

Gnomad EAS AF: 0.00657

Gnomad SAS AF: 0.0765

Gnomad FIN AF: 0.00128

Gnomad MID AF: 0.00333

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0208

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

GnomAD4 genome AF: 0.0251 AC: 3401 AN: 135456 Hom.: 75 Cov.: 26 AF XY: 0.0265 AC XY: 1708 AN XY: 64388

African (AFR) AF: 0.0533 AC: 1922 AN: 36080

American (AMR) AF: 0.0144 AC: 169 AN: 11720

Ashkenazi Jewish (ASJ) AF: 0.0244 AC: 82 AN: 3356

East Asian (EAS) AF: 0.00659 AC: 33 AN: 5006

South Asian (SAS) AF: 0.0765 AC: 357 AN: 4668

European-Finnish (FIN) AF: 0.00128 AC: 8 AN: 6232

Middle Eastern (MID) AF: 0.00365 AC: 1 AN: 274

European-Non Finnish (NFE) AF: 0.0121 AC: 793 AN: 65472

Other (OTH) AF: 0.0202 AC: 36 AN: 1786

Alfa AF: 0.0195 Hom.: 6

Bravo AF: 0.0249

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs201427795; hg19: chr7-135255698;