Variant 5-37294371-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_153485.3(NUP155):c.3888A>G(p.Leu1296=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 1,597,574 control chromosomes in the GnomAD database, including 68,437 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5186 hom., cov: 31)

Exomes 𝑓: 0.29 ( 63251 hom. )

Consequence

NUP155
NM_153485.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.05

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 5-37294371-T-C is Benign according to our data. Variant chr5-37294371-T-C is described in ClinVar as [Benign]. Clinvar id is 1294896.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
NUP155	NM_153485.3 linkuse as main transcript	c.3888A>G	p.Leu1296=	synonymous_variant	33/35	ENST00000231498.8
NUP155	NM_004298.4 linkuse as main transcript	c.3711A>G	p.Leu1237=	synonymous_variant	33/35
NUP155	NM_001278312.2 linkuse as main transcript	c.3696A>G	p.Leu1232=	synonymous_variant	32/34

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP155	ENST00000231498.8 linkuse as main transcript	c.3888A>G	p.Leu1296=	synonymous_variant	33/35	1	NM_153485.3	P1	O75694-1
NUP155	ENST00000381843.6 linkuse as main transcript	c.3711A>G	p.Leu1237=	synonymous_variant	33/35	1			O75694-2
NUP155	ENST00000513532.1 linkuse as main transcript	c.3696A>G	p.Leu1232=	synonymous_variant	32/34	1
NUP155	ENST00000502533.5 linkuse as main transcript	n.1546A>G		non_coding_transcript_exon_variant	12/14	5

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37935

AN:

151924

Hom.:

5182

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.375

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.269

GnomAD3 exomes

AF:

0.294

AC:

73434

AN:

249696

Hom.:

11254

AF XY:

0.301

AC XY:

40574

AN XY:

134980

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.291

Gnomad ASJ exome

AF:

0.354

Gnomad EAS exome

AF:

0.388

Gnomad SAS exome

AF:

0.370

Gnomad FIN exome

AF:

0.224

Gnomad NFE exome

AF:

0.289

Gnomad OTH exome

AF:

0.313

GnomAD4 exome

AF:

0.292

AC:

421869

AN:

1445534

Hom.:

63251

Cov.:

AF XY:

0.295

AC XY:

212435

AN XY:

720062

show subpopulations

Gnomad4 AFR exome

AF:

0.124

Gnomad4 AMR exome

AF:

0.290

Gnomad4 ASJ exome

AF:

0.347

Gnomad4 EAS exome

AF:

0.382

Gnomad4 SAS exome

AF:

0.364

Gnomad4 FIN exome

AF:

0.225

Gnomad4 NFE exome

AF:

0.289

Gnomad4 OTH exome

AF:

0.303

GnomAD4 genome

AF:

0.250

AC:

37949

AN:

152040

Hom.:

5186

Cov.:

AF XY:

0.250

AC XY:

18593

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.134

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.362

Gnomad4 EAS

AF:

0.375

Gnomad4 SAS

AF:

0.368

Gnomad4 FIN

AF:

0.221

Gnomad4 NFE

AF:

0.292

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.286

Hom.:

10661

Bravo

AF:

0.250

Asia WGS

AF:

0.306

AC:

1065

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

NUP155-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 04, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

8.0

DANN

Benign

0.71

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