7-135571411-TA-T

Variant summary

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

The NM_015135.3(NUP205):c.171+179del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0282 in 135,426 control chromosomes in the GnomAD database, including 67 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.028 (67 hom., cov: 30)
• Consequence: NUP205 NM_015135.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.618

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 7-135571411-TA-T is Benign according to our data. Variant chr7-135571411-TA-T is described in ClinVar as [Benign]. Clinvar id is 1252099.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUP205	NM_015135.3	c.171+179del		intron_variant		ENST00000285968.11
NUP205	NM_001329434.2	c.-915+179del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP205	ENST00000285968.11	c.171+179del		intron_variant		1	NM_015135.3	P1
NUP205	ENST00000489493.1	n.426+179del		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0281 AC: 3811 AN: 135406 Hom.: 67 Cov.: 30

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0161

Gnomad ASJ AF: 0.0263

Gnomad EAS AF: 0.00740

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.00329

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0282 AC: 3813 AN: 135426 Hom.: 67 Cov.: 30 AF XY: 0.0298 AC XY: 1944 AN XY: 65282

Gnomad4 AFR AF: 0.0544

Gnomad4 AMR AF: 0.0161

Gnomad4 ASJ AF: 0.0263

Gnomad4 EAS AF: 0.00742

Gnomad4 SAS AF: 0.0818

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0160

Gnomad4 OTH AF: 0.0241

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

Apr 13, 2021

- -

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: rs563193250; hg19: chr7-135256159;