5-37292217-ATT-A

Position:

• chr5-37292217-ATT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_153485.3(NUP155):​c.4038-181_4038-180delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0473 in 143,726 control chromosomes in the GnomAD database, including 532 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.047 (532 hom., cov: 31)
• Consequence: NUP155 NM_153485.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.66

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 -10 ACMG points.

• BP6: Variant 5-37292217-ATT-A is Benign according to our data. Variant chr5-37292217-ATT-A is described in ClinVar as [Benign]. Clinvar id is 1267101.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP155	NM_153485.3	c.4038-181_4038-180delAA		intron_variant		ENST00000231498.8	NP_705618.1
NUP155	NM_004298.4	c.3861-181_3861-180delAA		intron_variant			NP_004289.1
NUP155	NM_001278312.2	c.3846-181_3846-180delAA		intron_variant			NP_001265241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP155	ENST00000231498.8	c.4038-181_4038-180delAA		intron_variant		1	NM_153485.3	ENSP00000231498.3

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 6788 AN: 143706 Hom.: 530 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000442

Gnomad FIN AF: 0.000224

Gnomad MID AF: 0.0133

Gnomad NFE AF: 0.000661

Gnomad OTH AF: 0.0293

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

GnomAD4 genome AF: 0.0473 AC: 6797 AN: 143726 Hom.: 532 Cov.: 31 AF XY: 0.0454 AC XY: 3172 AN XY: 69874

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0146

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000444

Gnomad4 FIN AF: 0.000224

Gnomad4 NFE AF: 0.000661

Gnomad4 OTH AF: 0.0292

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

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: rs879236027; hg19: chr5-37292319;