Variant chr5-37293113-A-G 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.3931-128T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 669,844 control chromosomes in the GnomAD database, including 9,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 1981 hom., cov: 32)

Exomes 𝑓: 0.16 ( 7247 hom. )

Consequence

NUP155
NM_153485.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.838

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=-0.91).

BP6

Variant 5-37293113-A-G is Benign according to our data. Variant chr5-37293113-A-G is described in ClinVar as [Benign]. Clinvar id is 1251251.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
NUP155	NM_153485.3 linkuse as main transcript	c.3931-128T>C	intron_variant	ENST00000231498.8
NUP155	NM_001278312.2 linkuse as main transcript	c.3739-128T>C	intron_variant
NUP155	NM_004298.4 linkuse as main transcript	c.3754-128T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP155	ENST00000231498.8 linkuse as main transcript	c.3931-128T>C		intron_variant		1	NM_153485.3	P1	O75694-1

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24236

AN:

152084

Hom.:

1971

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.0724

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.169

GnomAD4 exome

AF:

0.163

AC:

84189

AN:

517642

Hom.:

7247

Cov.:

AF XY:

0.165

AC XY:

46283

AN XY:

280374

show subpopulations

Gnomad4 AFR exome

AF:

0.147

Gnomad4 AMR exome

AF:

0.189

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.0970

Gnomad4 SAS exome

AF:

0.199

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.154

GnomAD4 genome

AF:

0.160

AC:

24277

AN:

152202

Hom.:

1981

Cov.:

AF XY:

0.163

AC XY:

12159

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.180

Gnomad4 ASJ

AF:

0.179

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.200

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.178

Alfa

AF:

0.156

Hom.:

238

Bravo

AF:

0.155

Asia WGS

AF:

0.228

AC:

788

AN:

3470

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 14, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.20

DANN

Benign

0.70

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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