7-135571279-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015135.3(NUP205):c.171+45del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 953,788 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0013 (0 hom., cov: 28)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: NUP205 NM_015135.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.58

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 7-135571279-AT-A is Benign according to our data. Variant chr7-135571279-AT-A is described in ClinVar as [Benign]. Clinvar id is 1280600.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUP205	NM_015135.3	c.171+45del		intron_variant		ENST00000285968.11
NUP205	NM_001329434.2	c.-915+45del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP205	ENST00000285968.11	c.171+45del		intron_variant		1	NM_015135.3	P1
NUP205	ENST00000489493.1	n.426+45del		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.00129 AC: 178 AN: 138292 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.000503

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000954

Gnomad ASJ AF: 0.00213

Gnomad EAS AF: 0.00147

Gnomad SAS AF: 0.000223

Gnomad FIN AF: 0.00276

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00170

Gnomad OTH AF: 0.000534

GnomAD3 exomes AF: 0.310 AC: 18179 AN: 58698 Hom.: 0 AF XY: 0.324 AC XY: 10520 AN XY: 32468

Gnomad AFR exome AF: 0.234

Gnomad AMR exome AF: 0.389

Gnomad ASJ exome AF: 0.306

Gnomad EAS exome AF: 0.321

Gnomad SAS exome AF: 0.300

Gnomad FIN exome AF: 0.279

Gnomad NFE exome AF: 0.315

Gnomad OTH exome AF: 0.313

GnomAD4 exome AF: 0.185 AC: 150948 AN: 815478 Hom.: 0 Cov.: 0 AF XY: 0.189 AC XY: 74835 AN XY: 395524

Gnomad4 AFR exome AF: 0.174

Gnomad4 AMR exome AF: 0.278

Gnomad4 ASJ exome AF: 0.217

Gnomad4 EAS exome AF: 0.262

Gnomad4 SAS exome AF: 0.171

Gnomad4 FIN exome AF: 0.255

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.196

GnomAD4 genome AF: 0.00129 AC: 179 AN: 138310 Hom.: 0 Cov.: 28 AF XY: 0.00161 AC XY: 108 AN XY: 66946

Gnomad4 AFR AF: 0.000502

Gnomad4 AMR AF: 0.000953

Gnomad4 ASJ AF: 0.00213

Gnomad4 EAS AF: 0.00147

Gnomad4 SAS AF: 0.000225

Gnomad4 FIN AF: 0.00276

Gnomad4 NFE AF: 0.00170

Gnomad4 OTH AF: 0.00106

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

Jul 14, 2020

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs546492942; hg19: chr7-135256027;