NM_024923.4:c.818-721C>T

Variant names:

• chr3-13380442-G-A
• rs9310422
• NM_024923.4:c.818-721C>T

Variant summary

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

The NM_024923.4(NUP210):​c.818-721C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,098 control chromosomes in the GnomAD database, including 31,094 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 (31094 hom., cov: 32)
• Consequence: NUP210 NM_024923.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 4 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=-0.99).
• 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.818-721C>T		intron_variant	Intron 6 of 39	ENST00000254508.7	NP_079199.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP210	ENST00000254508.7	c.818-721C>T		intron_variant	Intron 6 of 39	2	NM_024923.4	ENSP00000254508.5
NUP210	ENST00000420141.3	n.901-721C>T		intron_variant	Intron 6 of 19	1

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94601 AN: 151980 Hom.: 31035 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.623 AC: 94729 AN: 152098 Hom.: 31094 Cov.: 32 AF XY: 0.616 AC XY: 45800 AN XY: 74348

African (AFR) AF: 0.848 AC: 35218 AN: 41514

American (AMR) AF: 0.506 AC: 7732 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2087 AN: 3472

East Asian (EAS) AF: 0.417 AC: 2158 AN: 5172

South Asian (SAS) AF: 0.454 AC: 2188 AN: 4822

European-Finnish (FIN) AF: 0.481 AC: 5088 AN: 10572

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

European-Non Finnish (NFE) AF: 0.563 AC: 38236 AN: 67962

Other (OTH) AF: 0.630 AC: 1332 AN: 2114

Alfa AF: 0.595 Hom.: 5291

Bravo AF: 0.637

Asia WGS AF: 0.505 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.34
PhyloP100		-0.30
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: rs9310422; hg19: chr3-13421942;