dbSNP rs1361037: NXTAR:n.81+4063C>T (chrX-67780747-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The XR_938423.3(NXTAR):n.81+4063C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.87 ( 30731 hom., 29336 hem., cov: 24)

Failed GnomAD Quality Control

Consequence

NXTAR
XR_938423.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.828

Publications

1 publications found

Variant links:

Genes affected

NXTAR (HGNC:56212): (negative expression of androgen receptor regulating lncRNA)

NXTAR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXTAR	XR_938423.3 link	n.81+4063C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.868

AC:

96695

AN:

111350

Hom.:

30741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.544

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.951

Gnomad ASJ

AF:

0.999

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.997

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.966

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.908

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.868

AC:

96708

AN:

111401

Hom.:

30731

Cov.:

AF XY:

0.874

AC XY:

29336

AN XY:

33575

show subpopulations

African (AFR)

AF:

0.544

AC:

16664

AN:

30632

American (AMR)

AF:

0.951

AC:

9988

AN:

10498

Ashkenazi Jewish (ASJ)

AF:

0.999

AC:

2645

AN:

2647

East Asian (EAS)

AF:

1.00

AC:

3512

AN:

3512

South Asian (SAS)

AF:

0.997

AC:

2597

AN:

2606

European-Finnish (FIN)

AF:

1.00

AC:

5977

AN:

5977

Middle Eastern (MID)

AF:

0.963

AC:

206

AN:

214

European-Non Finnish (NFE)

AF:

0.999

AC:

53042

AN:

53100

Other (OTH)

AF:

0.910

AC:

1389

AN:

1527

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

300

600

899

1199

1499

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.917

Hom.:

9439

Bravo

AF:

0.851

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.3

(source)

DANN

Benign

0.58

PhyloP100

0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over