7-135570950-A-ATAGT

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

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: 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

Gnomad4 AFR AF: 0.0533

Gnomad4 AMR AF: 0.0144

Gnomad4 ASJ AF: 0.0244

Gnomad4 EAS AF: 0.00659

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.00128

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.0202

Alfa AF: 0.0195 Hom.: 6

Bravo AF: 0.0249

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 08, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201427795; hg19: chr7-135255698;