Variant 1-154023201-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000368559.8(NUP210L):c.4219A>G(p.Thr1407Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

NUP210L
ENST00000368559.8 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.36

Variant links:

Genes affected

NUP210L (HGNC:29915): (nucleoporin 210 like) Predicted to act upstream of or within Sertoli cell development and spermatid development. Predicted to be integral component of membrane. Predicted to be part of nuclear pore. [provided by Alliance of Genome Resources, Apr 2022]

NUP210L links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.2448332).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP210L	NM_207308.3 linkuse as main transcript	c.4219A>G	p.Thr1407Ala	missense_variant	31/40	ENST00000368559.8	NP_997191.2
NUP210L	XM_011510122.2 linkuse as main transcript	c.4087A>G	p.Thr1363Ala	missense_variant	30/39		XP_011508424.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP210L	ENST00000368559.8 linkuse as main transcript	c.4219A>G	p.Thr1407Ala	missense_variant	31/40	5	NM_207308.3	ENSP00000357547	P2	Q5VU65-1
NUP210L	ENST00000368553.5 linkuse as main transcript	c.1018A>G	p.Thr340Ala	missense_variant	9/16	1		ENSP00000357541	A2
NUP210L	ENST00000271854.3 linkuse as main transcript	c.4219A>G	p.Thr1407Ala	missense_variant	31/38	5		ENSP00000271854	A2	Q5VU65-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000342

AC:

AN:

1461768

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.000149

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 03, 2022

The c.4219A>G (p.T1407A) alteration is located in exon 31 (coding exon 31) of the NUP210L gene. This alteration results from a A to G substitution at nucleotide position 4219, causing the threonine (T) at amino acid position 1407 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.22

T;T;.

Eigen

Benign

-0.12

Eigen_PC

Benign

0.014

FATHMM_MKL

Uncertain

0.81

LIST_S2

Benign

0.59

T;T;T

M_CAP

Benign

0.0072

MetaRNN

Benign

0.24

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.4

M;.;M

MutationTaster

Benign

0.83

N;N;N

PrimateAI

Uncertain

0.49

PROVEAN

Uncertain

-2.7

D;D;D

REVEL

Benign

0.075

Sift

Benign

0.061

T;T;T

Sift4G

Benign

0.11

T;T;T

Polyphen

0.0010

B;.;.

Vest4

0.27

MutPred

0.45

Loss of stability (P = 0.0543);.;Loss of stability (P = 0.0543);

MVP

0.54

MPC

0.29

ClinPred

0.84

GERP RS

4.2

Varity_R

0.12

gMVP

0.53

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over