rs779636166

Variant names:

• chr3-13319092-C-A
• rs779636166
• NM_024923.4:c.5543G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-13319092-C-A
• chr3-13319092-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_024923.4(NUP210):​c.5543G>T​(p.Ser1848Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1848N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NUP210 NM_024923.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.29519537).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP210	NM_024923.4	c.5543G>T	p.Ser1848Ile	missense_variant	Exon 39 of 40	ENST00000254508.7	NP_079199.2
NUP210	XM_047447795.1	c.2927G>T	p.Ser976Ile	missense_variant	Exon 21 of 22		XP_047303751.1
NUP210	XM_047447797.1	c.2894G>T	p.Ser965Ile	missense_variant	Exon 21 of 22		XP_047303753.1
NUP210	XM_047447796.1	c.2858G>T	p.Ser953Ile	missense_variant	Exon 21 of 22		XP_047303752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP210	ENST00000254508.7	c.5543G>T	p.Ser1848Ile	missense_variant	Exon 39 of 40	2	NM_024923.4	ENSP00000254508.5
NUP210	ENST00000695489.1	n.1271G>T		non_coding_transcript_exon_variant	Exon 3 of 4
NUP210	ENST00000695490.1	n.*971G>T		non_coding_transcript_exon_variant	Exon 21 of 22			ENSP00000511960.1
NUP210	ENST00000695490.1	n.*971G>T		3_prime_UTR_variant	Exon 21 of 22			ENSP00000511960.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.052	T
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.72	T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.30	T
MetaSVM	Benign	-1.2	T
MutationAssessor	Uncertain	2.4	M
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-2.0	N
REVEL	Benign	0.057
Sift	Benign	0.032	D
Sift4G	Uncertain	0.040	D
Polyphen		0.97	D
Vest4		0.38
MutPred		0.24		Loss of glycosylation at P1845 (P = 0.0213);
MVP		0.56
MPC		0.30
ClinPred		0.80	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.14
gMVP		0.71

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: rs779636166; hg19: chr3-13360592;