rs11039402

chr11-47804538-A-Cchr11-47804538-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_015231.3(NUP160):c.2574+11T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 1,512,470 control chromosomes in the GnomAD database, including 144,843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.35 (10568 hom., cov: 33)
  • Exomes 𝑓: 0.44 (134275 hom.)
• Consequence: NUP160 NM_015231.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.173

Genes affected

NUP160 (HGNC:18017): (nucleoporin 160) A structural constituent of nuclear pore. Involved in mRNA export from nucleus and nephron development. Part of nuclear pore outer ring. Colocalizes with kinetochore. Implicated in nephrotic syndrome type 19. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP6: Variant 11-47804538-A-C is Benign according to our data. Variant chr11-47804538-A-C is described in ClinVar as [Benign]. Clinvar id is 1327015.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUP160	NM_015231.3	c.2574+11T>G		intron_variant		ENST00000378460.7
NUP160	NR_134636.3	n.2621+11T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP160	ENST00000378460.7	c.2574+11T>G		intron_variant		1	NM_015231.3	P1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52688 AN: 152034 Hom.: 10569 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.400

GnomAD3 exomes AF: 0.407 AC: 74952 AN: 184372 Hom.: 16353 AF XY: 0.422 AC XY: 42921 AN XY: 101656

Gnomad AFR exome AF: 0.148

Gnomad AMR exome AF: 0.238

Gnomad ASJ exome AF: 0.478

Gnomad EAS exome AF: 0.379

Gnomad SAS exome AF: 0.537

Gnomad FIN exome AF: 0.348

Gnomad NFE exome AF: 0.453

Gnomad OTH exome AF: 0.425

GnomAD4 exome AF: 0.437 AC: 594823 AN: 1360318 Hom.: 134275 Cov.: 24 AF XY: 0.441 AC XY: 298505 AN XY: 676610

Gnomad4 AFR exome AF: 0.132

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.489

Gnomad4 EAS exome AF: 0.311

Gnomad4 SAS exome AF: 0.529

Gnomad4 FIN exome AF: 0.360

Gnomad4 NFE exome AF: 0.451

Gnomad4 OTH exome AF: 0.431

GnomAD4 genome AF: 0.346 AC: 52682 AN: 152152 Hom.: 10568 Cov.: 33 AF XY: 0.343 AC XY: 25505 AN XY: 74392

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.396

Alfa AF: 0.338 Hom.: 2048

Bravo AF: 0.333

Asia WGS AF: 0.466 AC: 1620 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Nephrotic syndrome, type 19 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	12
Dann	Benign	0.89
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs11039402; hg19: chr11-47826090; COSMIC: COSV65854472; COSMIC: COSV65854472;