5-37292137-G-A

Position:

• chr5-37292137-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_153485.3(NUP155):​c.4038-99C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,116,492 control chromosomes in the GnomAD database, including 34,717 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.34 (13827 hom., cov: 33)
  • Exomes 𝑓: 0.18 (20890 hom.)
• Consequence: NUP155 NM_153485.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.138

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 5-37292137-G-A is Benign according to our data. Variant chr5-37292137-G-A is described in ClinVar as [Benign]. Clinvar id is 1290619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP155	NM_153485.3	c.4038-99C>T		intron_variant		ENST00000231498.8	NP_705618.1
NUP155	NM_004298.4	c.3861-99C>T		intron_variant			NP_004289.1
NUP155	NM_001278312.2	c.3846-99C>T		intron_variant			NP_001265241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP155	ENST00000231498.8	c.4038-99C>T		intron_variant		1	NM_153485.3	ENSP00000231498.3

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51033 AN: 151964 Hom.: 13778 Cov.: 33

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.303

GnomAD4 exome AF: 0.182 AC: 175092 AN: 964414 Hom.: 20890 AF XY: 0.181 AC XY: 90283 AN XY: 499408

Gnomad4 AFR exome AF: 0.770

Gnomad4 AMR exome AF: 0.230

Gnomad4 ASJ exome AF: 0.182

Gnomad4 EAS exome AF: 0.0981

Gnomad4 SAS exome AF: 0.208

Gnomad4 FIN exome AF: 0.201

Gnomad4 NFE exome AF: 0.157

Gnomad4 OTH exome AF: 0.203

GnomAD4 genome AF: 0.336 AC: 51148 AN: 152078 Hom.: 13827 Cov.: 33 AF XY: 0.335 AC XY: 24893 AN XY: 74350

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.311

Alfa AF: 0.272 Hom.: 1539

Bravo AF: 0.356

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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	-0.96
CADD	Benign	3.2
DANN	Benign	0.26

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: rs216392; hg19: chr5-37292239; COSMIC: COSV51533712;