3-13360650-C-T

Variant names:

• chr3-13360650-C-T
• rs877511
• NM_024923.4:c.1933-159G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024923.4(NUP210):​c.1933-159G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,052 control chromosomes in the GnomAD database, including 31,054 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 0.62 (31054 hom., cov: 32)
• Consequence: NUP210 NM_024923.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 3 publications found

Genes affected

NUP210 (HGNC:30052): (nucleoporin 210) 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 membrane-spanning glycoprotein that is a major component of the nuclear pore complex. Multiple pseudogenes related to this gene are located on chromosome 3. [provided by RefSeq, Jul 2013]

NUP210 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP210	NM_024923.4	c.1933-159G>A		intron_variant	Intron 14 of 39	ENST00000254508.7	NP_079199.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP210	ENST00000254508.7	c.1933-159G>A		intron_variant	Intron 14 of 39	2	NM_024923.4	ENSP00000254508.5
NUP210	ENST00000420141.3	n.2016-159G>A		intron_variant	Intron 14 of 19	1
NUP210	ENST00000695491.1	n.-225G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94491 AN: 151934 Hom.: 30994 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.622 AC: 94621 AN: 152052 Hom.: 31054 Cov.: 32 AF XY: 0.616 AC XY: 45749 AN XY: 74328

African (AFR) AF: 0.848 AC: 35206 AN: 41510

American (AMR) AF: 0.506 AC: 7727 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2073 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2145 AN: 5162

South Asian (SAS) AF: 0.455 AC: 2190 AN: 4816

European-Finnish (FIN) AF: 0.481 AC: 5078 AN: 10568

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38188 AN: 67936

Other (OTH) AF: 0.631 AC: 1333 AN: 2112

Alfa AF: 0.603 Hom.: 4161

Bravo AF: 0.636

Asia WGS AF: 0.505 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.54
PhyloP100		-1.3
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: rs877511; hg19: chr3-13402150;