Variant rs3826777 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016553.5(NUP62):c.-199-316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,132 control chromosomes in the GnomAD database, including 9,190 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9188 hom., cov: 31)

Exomes 𝑓: 0.27 ( 2 hom. )

Consequence

NUP62
NM_016553.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.200

Variant links:

Genes affected

NUP62 (HGNC:8066): (nucleoporin 62) The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene is a member of the FG-repeat containing nucleoporins and is localized to the nuclear pore central plug. This protein associates with the importin alpha/beta complex which is involved in the import of proteins containing nuclear localization signals. Multiple transcript variants of this gene encode a single protein isoform. [provided by RefSeq, Jul 2008]

NUP62 links:

IL4I1 (HGNC:19094): (interleukin 4 induced 1) This gene encodes a secreted L-amino acid oxidase protein which primarily catabolizes L-phenylalanine and, to a lesser extent, L-arginine. The expression of this gene is induced by the cytokine interleukin 4 in B cells. This gene is also expressed in macrophages and dendritic cells. This protein may play a role immune system escape as it is expressed in tumor-associated macrophages and suppresses T-cell responses. This protein also contains domains thought to be involved in the binding of flavin adenine dinucleotide (FAD) cofactor. Multiple transcript variants encoding different isoforms have been found for this gene. Some transcripts of this gene share a promoter and exons of the 5' UTR with the overlapping NUP62 gene. [provided by RefSeq, Jul 2020]

IL4I1 links:

ENSG00000269179 (HGNC:):

ENSG00000269179 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP62	NM_016553.5 link	c.-199-316C>T		intron_variant		ENST00000352066.8	NP_057637.2	P37198A0A024QZF1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP62	ENST00000352066.8 link	c.-199-316C>T		intron_variant		1	NM_016553.5	ENSP00000305503.3		P37198
ENSG00000269179	ENST00000451973.1 link	n.*78-18247C>T		intron_variant		2		ENSP00000391489.1		H7BZU6

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51799

AN:

151944

Hom.:

9189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.442

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.366

Gnomad OTH

AF:

0.347

GnomAD4 exome

AF:

0.271

AC:

AN:

Hom.:

Cov.:

AF XY:

0.260

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.289

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.341

AC:

51814

AN:

152062

Hom.:

9188

Cov.:

AF XY:

0.345

AC XY:

25634

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.418

Gnomad4 ASJ

AF:

0.279

Gnomad4 EAS

AF:

0.430

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.442

Gnomad4 NFE

AF:

0.366

Gnomad4 OTH

AF:

0.348

Alfa

AF:

0.358

Hom.:

4705

Bravo

AF:

0.336

Asia WGS

AF:

0.359

AC:

1247

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.5

DANN

Benign

0.70

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over