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GeneBe

rs9310422

Variant summary

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

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.300
Variant links:
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]

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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=-0.99).
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/exons MANE UniProt
NUP210NM_024923.4 linkuse as main transcriptc.818-721C>T intron_variant ENST00000254508.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NUP210ENST00000254508.7 linkuse as main transcriptc.818-721C>T intron_variant 2 NM_024923.4 P1Q8TEM1-1
NUP210ENST00000420141.3 linkuse as main transcriptn.901-721C>T intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.622
AC:
94601
AN:
151980
Hom.:
31035
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.848
Gnomad4 AMR
AF:
0.506
Gnomad4 ASJ
AF:
0.601
Gnomad4 EAS
AF:
0.417
Gnomad4 SAS
AF:
0.454
Gnomad4 FIN
AF:
0.481
Gnomad4 NFE
AF:
0.563
Gnomad4 OTH
AF:
0.630
Alfa
AF:
0.589
Hom.:
5019
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

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.

Other links and lift over

dbSNP: rs9310422; hg19: chr3-13421942; API