5-37292265-C-G

Position:

• chr5-37292265-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_153485.3(NUP155):​c.4038-227G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,006 control chromosomes in the GnomAD database, including 22,365 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.51 (22365 hom., cov: 28)
• Consequence: NUP155 NM_153485.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.82

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BP6: Variant 5-37292265-C-G is Benign according to our data. Variant chr5-37292265-C-G is described in ClinVar as [Benign]. Clinvar id is 1263135.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP155	NM_153485.3	c.4038-227G>C		intron_variant		ENST00000231498.8	NP_705618.1
NUP155	NM_004298.4	c.3861-227G>C		intron_variant			NP_004289.1
NUP155	NM_001278312.2	c.3846-227G>C		intron_variant			NP_001265241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP155	ENST00000231498.8	c.4038-227G>C		intron_variant		1	NM_153485.3	ENSP00000231498.3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 76772 AN: 150894 Hom.: 22303 Cov.: 28

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.505

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.509 AC: 76890 AN: 151006 Hom.: 22365 Cov.: 28 AF XY: 0.509 AC XY: 37530 AN XY: 73696

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.512

Alfa AF: 0.261 Hom.: 580

Bravo AF: 0.526

Asia WGS AF: 0.466 AC: 1619 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-1.0
CADD	Benign	0.51
DANN	Benign	0.76

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

Other links and lift over

dbSNP: rs216393; hg19: chr5-37292367;