NM_014669.5:c.490-3080G>A

Variant names:

• chr16-56815584-G-A
• rs1529929
• NM_014669.5:c.490-3080G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014669.5(NUP93):​c.490-3080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,032 control chromosomes in the GnomAD database, including 14,437 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (14437 hom., cov: 32)
• Consequence: NUP93 NM_014669.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 7 publications found

Genes affected

NUP93 (HGNC:28958): (nucleoporin 93) The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. This gene encodes a nucleoporin protein that localizes both to the basket of the pore and to the nuclear entry of the central gated channel of the pore. The encoded protein is a target of caspase cysteine proteases that play a central role in programmed cell death by apoptosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]

NUP93 Gene-Disease associations (from GenCC):

• nephrotic syndrome, type 12

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Laboratory for Molecular Medicine
• familial idiopathic steroid-resistant nephrotic syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP93	NM_014669.5	c.490-3080G>A		intron_variant	Intron 5 of 21	ENST00000308159.10	NP_055484.3
NUP93	NM_001242795.2	c.121-3080G>A		intron_variant	Intron 3 of 19		NP_001229724.1
NUP93	NM_001242796.2	c.121-3080G>A		intron_variant	Intron 3 of 19		NP_001229725.1
NUP93	XM_005256263.4	c.490-3080G>A		intron_variant	Intron 5 of 21		XP_005256320.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP93	ENST00000308159.10	c.490-3080G>A		intron_variant	Intron 5 of 21	1	NM_014669.5	ENSP00000310668.5

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65757 AN: 151914 Hom.: 14441 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.433 AC: 65784 AN: 152032 Hom.: 14437 Cov.: 32 AF XY: 0.434 AC XY: 32258 AN XY: 74326

African (AFR) AF: 0.456 AC: 18894 AN: 41426

American (AMR) AF: 0.417 AC: 6376 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1439 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3177 AN: 5174

South Asian (SAS) AF: 0.525 AC: 2529 AN: 4818

European-Finnish (FIN) AF: 0.328 AC: 3467 AN: 10580

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28507 AN: 67970

Other (OTH) AF: 0.447 AC: 944 AN: 2112

Alfa AF: 0.431 Hom.: 20019

Bravo AF: 0.441

Asia WGS AF: 0.535 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.032
DANN	Benign	0.64
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1529929; hg19: chr16-56849496;