Variant 5-37294294-G-T 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.3930+35C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00557 in 1,400,334 control chromosomes in the GnomAD database, including 381 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.029 ( 222 hom., cov: 31)

Exomes 𝑓: 0.0028 ( 159 hom. )

Consequence

NUP155
NM_153485.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.67

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:

NUP155 (HGNC:):

NUP155 links:

Genome browser will be placed here

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 5-37294294-G-T is Benign according to our data. Variant chr5-37294294-G-T is described in ClinVar as [Benign]. Clinvar id is 1247038.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
NUP155	NM_153485.3 linkuse as main transcript	c.3930+35C>A	intron_variant	ENST00000231498.8	NP_705618.1	O75694-1A0A024R071
NUP155	NM_004298.4 linkuse as main transcript	c.3753+35C>A	intron_variant		NP_004289.1	O75694-2
NUP155	NM_001278312.2 linkuse as main transcript	c.3738+35C>A	intron_variant		NP_001265241.1	E9PF10B4DLT2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
NUP155	ENST00000231498.8 linkuse as main transcript	c.3930+35C>A	intron_variant	1	NM_153485.3	ENSP00000231498.3	O75694-1
NUP155	ENST00000381843.6 linkuse as main transcript	c.3753+35C>A	intron_variant	1		ENSP00000371265.2	O75694-2
NUP155	ENST00000513532.1 linkuse as main transcript	c.3738+35C>A	intron_variant	1		ENSP00000422019.1	E9PF10
NUP155	ENST00000502533.5 linkuse as main transcript	n.1588+35C>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0286

AC:

4350

AN:

151836

Hom.:

222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0991

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0123

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.0250

GnomAD3 exomes

AF:

0.00606

AC:

933

AN:

153928

Hom.:

AF XY:

0.00450

AC XY:

367

AN XY:

81576

show subpopulations

Gnomad AFR exome

AF:

0.0985

Gnomad AMR exome

AF:

0.00498

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000314

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000117

Gnomad OTH exome

AF:

0.00186

GnomAD4 exome

AF:

0.00276

AC:

3446

AN:

1248380

Hom.:

159

Cov.:

AF XY:

0.00233

AC XY:

1453

AN XY:

622742

show subpopulations

Gnomad4 AFR exome

AF:

0.100

Gnomad4 AMR exome

AF:

0.00548

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000325

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000475

Gnomad4 OTH exome

AF:

0.00608

GnomAD4 genome

AF:

0.0287

AC:

4355

AN:

151954

Hom.:

222

Cov.:

AF XY:

0.0275

AC XY:

2046

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.0990

Gnomad4 AMR

AF:

0.0123

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000623

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000132

Gnomad4 OTH

AF:

0.0247

Alfa

AF:

0.0165

Hom.:

Bravo

AF:

0.0336

Asia WGS

AF:

0.00550

AC:

AN:

3466

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 13, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.018

DANN

Benign

0.60

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