NM_153485.3:c.4038-181_4038-180delAA

Variant names:

• chr5-37292217-ATT-A
• rs879236027
• NM_153485.3:c.4038-181_4038-180delAA

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• familial atrial fibrillation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• atrial fibrillation, familial, 15

  Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153485.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP155	NM_153485.3	MANE Select	c.4038-181_4038-180delAA		intron	N/A	NP_705618.1	O75694-1
	NUP155	NM_004298.4		c.3861-181_3861-180delAA		intron	N/A	NP_004289.1	O75694-2
	NUP155	NM_001278312.2		c.3846-181_3846-180delAA		intron	N/A	NP_001265241.1	E9PF10

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP155	ENST00000231498.8	TSL:1 MANE Select	c.4038-181_4038-180delAA		intron	N/A	ENSP00000231498.3	O75694-1
	NUP155	ENST00000381843.6	TSL:1	c.3861-181_3861-180delAA		intron	N/A	ENSP00000371265.2	O75694-2
	NUP155	ENST00000513532.1	TSL:1	c.3846-181_3846-180delAA		intron	N/A	ENSP00000422019.1	E9PF10

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

African (AFR) AF: 0.164 AC: 6481 AN: 39530

American (AMR) AF: 0.0146 AC: 208 AN: 14238

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3348

East Asian (EAS) AF: 0.00 AC: 0 AN: 4956

South Asian (SAS) AF: 0.000444 AC: 2 AN: 4502

European-Finnish (FIN) AF: 0.000224 AC: 2 AN: 8936

Middle Eastern (MID) AF: 0.0145 AC: 4 AN: 276

European-Non Finnish (NFE) AF: 0.000661 AC: 43 AN: 65090

Other (OTH) AF: 0.0292 AC: 57 AN: 1952

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs879236027; hg19: chr5-37292319;