rs1361037

Variant names:

• chrX-67780747-G-A
• rs1361037
• XR_938423.3:n.81+4063C>T

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.868 AC: 96695 AN: 111350 Hom.: 30741 Cov.: 24

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.: 24 AF XY: 0.874 AC XY: 29336 AN XY: 33575

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

Alfa AF: 0.917 Hom.: 9439

Bravo AF: 0.851

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.58
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1361037; hg19: chrX-67000589;