Genetic Variant NXF5:n.1220+50_1220+51insC (chrX-101838149-T-TG) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000263032.5(NXF5):n.1220+50_1220+51insC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 1.0 ( 683 hom., 19 hem., cov: 0)

Exomes 𝑓: 1.0 ( 91203 hom. 81145 hem. )

Failed GnomAD Quality Control

Consequence

NXF5
ENST00000263032.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.137

Publications

0 publications found

Variant links:

Genes affected

NXF5 (HGNC:):

NXF5 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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6

Variant X-101838149-T-TG is Benign according to our data. Variant chrX-101838149-T-TG is described in ClinVar as Benign. ClinVar VariationId is 1293800.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000263032.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
NXF5	NR_028089.1	n.1220+50dupC	intron	N/A
NXF5	NR_159736.1	n.1031+50dupC	intron	N/A
NXF5	NR_159737.1	n.1031+50dupC	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
NXF5	ENST00000263032.5	TSL:1	n.1220+50_1220+51insC	intron	N/A
NXF5	ENST00000332614.6	TSL:1	n.1031+50_1031+51insC	intron	N/A
NXF5	ENST00000361330.5	TSL:1	n.1031+50_1031+51insC	intron	N/A

Frequencies

GnomAD3 genomes

AF:

1.00

AC:

1391

AN:

1391

Hom.:

686

Cov.:

show subpopulations

Gnomad AFR

AF:

1.00

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

1.00

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

1.00

GnomAD2 exomes

AF:

0.999

AC:

40485

AN:

40515

AF XY:

1.00

show subpopulations

Gnomad AFR exome

AF:

1.00

Gnomad AMR exome

AF:

0.999

Gnomad ASJ exome

AF:

0.995

Gnomad EAS exome

AF:

1.00

Gnomad FIN exome

AF:

0.993

Gnomad NFE exome

AF:

1.00

Gnomad OTH exome

AF:

0.999

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

1.00

AC:

263565

AN:

263579

Hom.:

91203

Cov.:

AF XY:

1.00

AC XY:

81145

AN XY:

81145

show subpopulations

African (AFR)

AF:

1.00

AC:

8405

AN:

8405

American (AMR)

AF:

1.00

AC:

12629

AN:

12629

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

8098

AN:

8098

East Asian (EAS)

AF:

1.00

AC:

17328

AN:

17328

South Asian (SAS)

AF:

1.00

AC:

23851

AN:

23851

European-Finnish (FIN)

AF:

1.00

AC:

16499

AN:

16500

Middle Eastern (MID)

AF:

1.00

AC:

1090

AN:

1090

European-Non Finnish (NFE)

AF:

1.00

AC:

159628

AN:

159641

Other (OTH)

AF:

1.00

AC:

16037

AN:

16037

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.850

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

774

1548

2322

3096

3870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

1.00

AC:

1385

AN:

1385

Hom.:

683

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

314

AN:

314

American (AMR)

AF:

1.00

AC:

179

AN:

179

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

111

AN:

111

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

538

AN:

538

Other (OTH)

AF:

1.00

AC:

AN:

Age Distribution

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.766

Hom.:

5724

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.14

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over