dbSNP rs199849270: ENSG00000290798:n.697C>T (chrX-101841315-G-A) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The ENST00000263032.5(ENSG00000290798):n.697C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000423 in 1,206,403 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 160 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.00040 ( 0 hom., 12 hem., cov: 20)

Exomes 𝑓: 0.00043 ( 0 hom. 148 hem. )

Consequence

ENSG00000290798
ENST00000263032.5 non_coding_transcript_exon

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 1.91

Variant links:

Genes affected

ENSG00000290798 (HGNC:):

ENSG00000290798 links:

NXF5 (HGNC:8075): (nuclear RNA export factor 5) This gene is one member of a family of nuclear RNA export factor genes. Most transcript variants are candidates for nonsense-mediated decay (NMD) and may not express proteins in vivo. [provided by RefSeq, Sep 2022]

NXF5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.28517944).

BS2

High Hemizygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
NXF5	NR_028089.1 link	n.697C>T	non_coding_transcript_exon_variant	Exon 7 of 19
NXF5	NR_159736.1 link	n.508C>T	non_coding_transcript_exon_variant	Exon 5 of 17
NXF5	NR_159737.1 link	n.508C>T	non_coding_transcript_exon_variant	Exon 5 of 17

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290798	ENST00000263032.5 link	n.697C>T	non_coding_transcript_exon_variant	Exon 7 of 19	1
ENSG00000290798	ENST00000332614.6 link	n.508C>T	non_coding_transcript_exon_variant	Exon 5 of 17	1
ENSG00000290798	ENST00000361330.5 link	n.508C>T	non_coding_transcript_exon_variant	Exon 5 of 17	1

Frequencies

GnomAD3 genomes

AF:

0.000397

AC:

AN:

108436

Hom.:

Cov.:

AF XY:

0.000390

AC XY:

AN XY:

30758

show subpopulations

Gnomad AFR

AF:

0.000270

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000291

Gnomad SAS

AF:

0.00127

Gnomad FIN

AF:

0.00106

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000478

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000402

AC:

AN:

178929

Hom.:

AF XY:

0.000403

AC XY:

AN XY:

64481

show subpopulations

Gnomad AFR exome

AF:

0.0000802

Gnomad AMR exome

AF:

0.0000739

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000725

Gnomad SAS exome

AF:

0.000545

Gnomad FIN exome

AF:

0.00102

Gnomad NFE exome

AF:

0.000526

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000425

AC:

467

AN:

1097915

Hom.:

Cov.:

AF XY:

0.000407

AC XY:

148

AN XY:

363325

show subpopulations

Gnomad4 AFR exome

AF:

0.000379

Gnomad4 AMR exome

AF:

0.0000284

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000370

Gnomad4 FIN exome

AF:

0.00143

Gnomad4 NFE exome

AF:

0.000428

Gnomad4 OTH exome

AF:

0.000391

GnomAD4 genome

AF:

0.000396

AC:

AN:

108488

Hom.:

Cov.:

AF XY:

0.000389

AC XY:

AN XY:

30822

show subpopulations

Gnomad4 AFR

AF:

0.000269

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000292

Gnomad4 SAS

AF:

0.00127

Gnomad4 FIN

AF:

0.00106

Gnomad4 NFE

AF:

0.000478

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000648

Hom.:

Bravo

AF:

0.000321

ESP6500AA

AF:

0.000261

AC:

ESP6500EA

AF:

0.000150

AC:

ExAC

AF:

0.000453

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Focal segmental glomerulosclerosis

Uncertain:1

Sep 15, 2013

OMIM

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.13

BayesDel_noAF

Uncertain

-0.080

CADD

Benign

3.8

DANN

Benign

0.96

DEOGEN2

Benign

0.37

T;.

FATHMM_MKL

Benign

0.70

LIST_S2

Benign

0.69

T;T

M_CAP

Pathogenic

0.64

MetaRNN

Benign

0.29

T;T

MetaSVM

Benign

-0.86

MutationAssessor

Pathogenic

3.2

M;M

PrimateAI

Benign

0.47

PROVEAN

Pathogenic

-7.5

D;D

REVEL

Uncertain

0.34

Sift

Uncertain

0.0010

D;D

Sift4G

Pathogenic

0.0010

D;D

Vest4

0.20

MVP

0.78

MPC

1.8

ClinPred

0.16

GERP RS

-0.91

Varity_R

0.23

gMVP

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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