Variant chr17-5386713-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002532.6(NUP88):c.2157A>G(p.Lys719=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 1,594,484 control chromosomes in the GnomAD database, including 153,299 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 15298 hom., cov: 32)

Exomes 𝑓: 0.43 ( 138001 hom. )

Consequence

NUP88
NM_002532.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0130

Variant links:

Genes affected

NUP88 (HGNC:8067): (nucleoporin 88) 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, a family of 50 to 100 proteins, are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene belongs to the nucleoporin family and is associated with the oncogenic nucleoporin CAN/Nup214 in a dynamic subcomplex. This protein is also overexpressed in a large number of malignant neoplasms and precancerous dysplasias. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

NUP88 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 17-5386713-T-C is Benign according to our data. Variant chr17-5386713-T-C is described in ClinVar as [Benign]. Clinvar id is 1327043.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.013 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
NUP88	NM_002532.6 linkuse as main transcript	c.2157A>G	p.Lys719=	synonymous_variant	16/17	ENST00000573584.6
NUP88	NM_001320653.2 linkuse as main transcript	c.2205A>G	p.Lys735=	synonymous_variant	16/17
NUP88	XM_047436155.1 linkuse as main transcript	c.1812A>G	p.Lys604=	synonymous_variant	16/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP88	ENST00000573584.6 linkuse as main transcript	c.2157A>G	p.Lys719=	synonymous_variant	16/17	1	NM_002532.6	P1

Frequencies

GnomAD3 genomes

AF:

0.437

AC:

66423

AN:

151992

Hom.:

15289

Cov.:

show subpopulations

Gnomad AFR

AF:

0.415

Gnomad AMI

AF:

0.213

Gnomad AMR

AF:

0.413

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.837

Gnomad SAS

AF:

0.649

Gnomad FIN

AF:

0.588

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.392

Gnomad OTH

AF:

0.428

GnomAD3 exomes

AF:

0.477

AC:

119820

AN:

251288

Hom.:

30982

AF XY:

0.481

AC XY:

65335

AN XY:

135814

show subpopulations

Gnomad AFR exome

AF:

0.414

Gnomad AMR exome

AF:

0.431

Gnomad ASJ exome

AF:

0.392

Gnomad EAS exome

AF:

0.839

Gnomad SAS exome

AF:

0.634

Gnomad FIN exome

AF:

0.579

Gnomad NFE exome

AF:

0.388

Gnomad OTH exome

AF:

0.457

GnomAD4 exome

AF:

0.425

AC:

613504

AN:

1442374

Hom.:

138001

Cov.:

AF XY:

0.431

AC XY:

310067

AN XY:

718948

show subpopulations

Gnomad4 AFR exome

AF:

0.405

Gnomad4 AMR exome

AF:

0.429

Gnomad4 ASJ exome

AF:

0.382

Gnomad4 EAS exome

AF:

0.842

Gnomad4 SAS exome

AF:

0.622

Gnomad4 FIN exome

AF:

0.557

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.451

GnomAD4 genome

AF:

0.437

AC:

66476

AN:

152110

Hom.:

15298

Cov.:

AF XY:

0.452

AC XY:

33638

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.415

Gnomad4 AMR

AF:

0.413

Gnomad4 ASJ

AF:

0.388

Gnomad4 EAS

AF:

0.837

Gnomad4 SAS

AF:

0.648

Gnomad4 FIN

AF:

0.588

Gnomad4 NFE

AF:

0.392

Gnomad4 OTH

AF:

0.433

Alfa

AF:

0.397

Hom.:

6104

Bravo

AF:

0.421

Asia WGS

AF:

0.749

AC:

2600

AN:

3478

EpiCase

AF:

0.396

EpiControl

AF:

0.395

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Fetal akinesia deformation sequence 4

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

-0.67

CADD

Benign

8.4

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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