3-13360650-C-T

Position:

• chr3-13360650-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NUP210	NM_024923.4	c.1933-159G>A		intron_variant		ENST00000254508.7	NP_079199.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP210	ENST00000254508.7	c.1933-159G>A		intron_variant		2	NM_024923.4	ENSP00000254508	P1
NUP210	ENST00000420141.3	n.2016-159G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.631

Alfa AF: 0.595 Hom.: 3889

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

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: rs877511; hg19: chr3-13402150;