Variant rs217776 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_153485.3(NUP155):c.724-23G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,524,262 control chromosomes in the GnomAD database, including 39,416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 12380 hom., cov: 32)

Exomes 𝑓: 0.18 ( 27036 hom. )

Consequence

NUP155
NM_153485.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.315

Variant links:

Genes affected

NUP155 (HGNC:8063): (nucleoporin 155) Nucleoporins are proteins that play an important role in the assembly and functioning of the nuclear pore complex (NPC) which regulates the movement of macromolecules across the nuclear envelope (NE). The protein encoded by this gene plays a role in the fusion of NE vesicles and formation of the double membrane NE. The protein may also be involved in cardiac physiology and may be associated with the pathogenesis of atrial fibrillation. Alternative splicing results in multiple transcript variants of this gene. A pseudogene associated with this gene is located on chromosome 6. [provided by RefSeq, May 2013]

NUP155 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 5-37350288-C-A is Benign according to our data. Variant chr5-37350288-C-A is described in ClinVar as [Benign]. Clinvar id is 1180263.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP155	NM_153485.3 linkuse as main transcript	c.724-23G>T		intron_variant		ENST00000231498.8	NP_705618.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
NUP155	ENST00000231498.8 linkuse as main transcript	c.724-23G>T	intron_variant	1	NM_153485.3	ENSP00000231498	P1	O75694-1
NUP155	ENST00000381843.6 linkuse as main transcript	c.547-23G>T	intron_variant	1		ENSP00000371265		O75694-2
NUP155	ENST00000513532.1 linkuse as main transcript	c.724-23G>T	intron_variant	1		ENSP00000422019

Frequencies

GnomAD3 genomes

AF:

0.323

AC:

48985

AN:

151860

Hom.:

12343

Cov.:

show subpopulations

Gnomad AFR

AF:

0.710

Gnomad AMI

AF:

0.0724

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.180

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.201

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.291

GnomAD3 exomes

AF:

0.215

AC:

53837

AN:

250426

Hom.:

8110

AF XY:

0.204

AC XY:

27653

AN XY:

135396

show subpopulations

Gnomad AFR exome

AF:

0.716

Gnomad AMR exome

AF:

0.228

Gnomad ASJ exome

AF:

0.183

Gnomad EAS exome

AF:

0.116

Gnomad SAS exome

AF:

0.212

Gnomad FIN exome

AF:

0.206

Gnomad NFE exome

AF:

0.162

Gnomad OTH exome

AF:

0.190

GnomAD4 exome

AF:

0.176

AC:

241335

AN:

1372284

Hom.:

27036

Cov.:

AF XY:

0.176

AC XY:

120756

AN XY:

687612

show subpopulations

Gnomad4 AFR exome

AF:

0.725

Gnomad4 AMR exome

AF:

0.227

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.0982

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.201

Gnomad4 NFE exome

AF:

0.154

Gnomad4 OTH exome

AF:

0.196

GnomAD4 genome

AF:

0.323

AC:

49084

AN:

151978

Hom.:

12380

Cov.:

AF XY:

0.321

AC XY:

23866

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.709

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.180

Gnomad4 EAS

AF:

0.124

Gnomad4 SAS

AF:

0.209

Gnomad4 FIN

AF:

0.201

Gnomad4 NFE

AF:

0.160

Gnomad4 OTH

AF:

0.299

Alfa

AF:

0.164

Hom.:

914

Bravo

AF:

0.340

Asia WGS

AF:

0.260

AC:

902

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.30

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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