Variant rs11264875 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_207308.3(NUP210L):c.4471G>A(p.Val1491Ile) variant causes a missense change. The variant allele was found at a frequency of 0.29 in 1,613,150 control chromosomes in the GnomAD database, including 69,763 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.27 ( 5790 hom., cov: 31)

Exomes 𝑓: 0.29 ( 63973 hom. )

Consequence

NUP210L
NM_207308.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.25

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0064232945).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein	UniProt
NUP210L	NM_207308.3 linkuse as main transcript	c.4471G>A	p.Val1491Ile	missense_variant	32/40	NP_997191.2	Q5VU65-1
NUP210L	NM_001159484.1 linkuse as main transcript	c.4471G>A	p.Val1491Ile	missense_variant	32/38	NP_001152956.1	Q5VU65-2
NUP210L	XM_017002788.3 linkuse as main transcript	c.4471G>A	p.Val1491Ile	missense_variant	32/39	XP_016858277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
NUP210L	ENST00000368559.8 linkuse as main transcript	c.4471G>A	p.Val1491Ile	missense_variant	32/40	5	ENSP00000357547.3	Q5VU65-1
NUP210L	ENST00000368553.5 linkuse as main transcript	c.1270G>A	p.Val424Ile	missense_variant	10/16	1	ENSP00000357541.1	X6R6V8
NUP210L	ENST00000271854.3 linkuse as main transcript	c.4471G>A	p.Val1491Ile	missense_variant	32/38	5	ENSP00000271854.3	Q5VU65-2

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40581

AN:

151738

Hom.:

5782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.291

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.288

GnomAD3 exomes

AF:

0.313

AC:

77990

AN:

249556

Hom.:

12819

AF XY:

0.313

AC XY:

42370

AN XY:

135392

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.427

Gnomad ASJ exome

AF:

0.305

Gnomad EAS exome

AF:

0.267

Gnomad SAS exome

AF:

0.324

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.298

Gnomad OTH exome

AF:

0.327

GnomAD4 exome

AF:

0.293

AC:

427766

AN:

1461294

Hom.:

63973

Cov.:

AF XY:

0.295

AC XY:

214230

AN XY:

726988

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.420

Gnomad4 ASJ exome

AF:

0.297

Gnomad4 EAS exome

AF:

0.300

Gnomad4 SAS exome

AF:

0.320

Gnomad4 FIN exome

AF:

0.337

Gnomad4 NFE exome

AF:

0.287

Gnomad4 OTH exome

AF:

0.282

GnomAD4 genome

AF:

0.267

AC:

40620

AN:

151856

Hom.:

5790

Cov.:

AF XY:

0.273

AC XY:

20235

AN XY:

74164

show subpopulations

Gnomad4 AFR

AF:

0.167

Gnomad4 AMR

AF:

0.373

Gnomad4 ASJ

AF:

0.291

Gnomad4 EAS

AF:

0.283

Gnomad4 SAS

AF:

0.325

Gnomad4 FIN

AF:

0.336

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.286

Alfa

AF:

0.288

Hom.:

16997

Bravo

AF:

0.268

TwinsUK

AF:

0.297

AC:

1100

ALSPAC

AF:

0.279

AC:

1076

ESP6500AA

AF:

0.161

AC:

655

ESP6500EA

AF:

0.274

AC:

2291

ExAC

AF:

0.308

AC:

37211

Asia WGS

AF:

0.283

AC:

984

AN:

3478

EpiCase

AF:

0.297

EpiControl

AF:

0.305

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.11

T;T;.

Eigen

Uncertain

0.63

Eigen_PC

Uncertain

0.66

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.72

T;T;T

MetaRNN

Benign

0.0064

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.4

M;.;M

PrimateAI

Benign

0.42

PROVEAN

Benign

-0.62

N;N;N

REVEL

Benign

0.14

Sift

Benign

0.054

T;T;T

Sift4G

Uncertain

0.014

D;D;D

Polyphen

0.98

D;.;.

Vest4

0.24

MPC

0.53

ClinPred

0.021

GERP RS

6.1

Varity_R

0.10

gMVP

0.66

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over