7-135570857-T-TATATAA

Variant summary

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

The NM_015135.3(NUP205):c.29-240_29-235dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.021 (86 hom., cov: 19)
• Consequence: NUP205 NM_015135.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.00

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 7-135570857-T-TATATAA is Benign according to our data. Variant chr7-135570857-T-TATATAA is described in ClinVar as [Likely_benign]. Clinvar id is 1317815.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUP205	NM_015135.3	c.29-240_29-235dup		intron_variant		ENST00000285968.11
NUP205	NM_001329434.2	c.-1057-240_-1057-235dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP205	ENST00000285968.11	c.29-240_29-235dup		intron_variant		1	NM_015135.3	P1
NUP205	ENST00000489493.1	n.284-240_284-235dup		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 2459 AN: 115056 Hom.: 86 Cov.: 19

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.00459

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.000567

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0100

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0214 AC: 2461 AN: 115044 Hom.: 86 Cov.: 19 AF XY: 0.0235 AC XY: 1241 AN XY: 52862

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.0109

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.00461

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.000567

Gnomad4 NFE AF: 0.0100

Gnomad4 OTH AF: 0.0219

Alfa AF: 0.0177 Hom.: 2

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 03, 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: rs1264298142; hg19: chr7-135255605;