Variant chr16-56798390-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014669.5(NUP93):c.298-86C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,090,826 control chromosomes in the GnomAD database, including 8,256 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 1385 hom., cov: 32)

Exomes 𝑓: 0.12 ( 6871 hom. )

Consequence

NUP93
NM_014669.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.53

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 16-56798390-C-T is Benign according to our data. Variant chr16-56798390-C-T is described in ClinVar as [Benign]. Clinvar id is 1233605.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
NUP93	NM_014669.5 linkuse as main transcript	c.298-86C>T	intron_variant	ENST00000308159.10
NUP93	NM_001242795.2 linkuse as main transcript	c.-72-86C>T	intron_variant
NUP93	NM_001242796.2 linkuse as main transcript	c.-72-86C>T	intron_variant
NUP93	XM_005256263.4 linkuse as main transcript	c.298-86C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP93	ENST00000308159.10 linkuse as main transcript	c.298-86C>T		intron_variant		1	NM_014669.5	P1	Q8N1F7-1

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19805

AN:

152020

Hom.:

1384

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.0680

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.0953

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.128

GnomAD4 exome

AF:

0.116

AC:

108937

AN:

938688

Hom.:

6871

AF XY:

0.118

AC XY:

57457

AN XY:

485764

show subpopulations

Gnomad4 AFR exome

AF:

0.179

Gnomad4 AMR exome

AF:

0.0749

Gnomad4 ASJ exome

AF:

0.0636

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.160

Gnomad4 FIN exome

AF:

0.0971

Gnomad4 NFE exome

AF:

0.112

Gnomad4 OTH exome

AF:

0.117

GnomAD4 genome

AF:

0.130

AC:

19821

AN:

152138

Hom.:

1385

Cov.:

AF XY:

0.130

AC XY:

9665

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.114

Gnomad4 ASJ

AF:

0.0680

Gnomad4 EAS

AF:

0.139

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.0953

Gnomad4 NFE

AF:

0.114

Gnomad4 OTH

AF:

0.127

Alfa

AF:

0.117

Hom.:

1869

Bravo

AF:

0.131

Asia WGS

AF:

0.152

AC:

530

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.0080

DANN

Benign

0.30

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over