rs1337082

Variant names:

• chrX-67764173-G-A
• rs1337082
• XR_938423.3:n.82-2207C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-67764173-G-A
• chrX-67764173-G-C

Variant summary

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

The XR_938423.3(NXTAR):​n.82-2207C>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 0.63 (18384 hom., 21525 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: NXTAR XR_938423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 8 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=-0.94).

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: 0.627 AC: 69698 AN: 111141 Hom.: 18392 Cov.: 24

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.661

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: 0.627 AC: 69690 AN: 111197 Hom.: 18384 Cov.: 24 AF XY: 0.644 AC XY: 21525 AN XY: 33407

African (AFR) AF: 0.152 AC: 4655 AN: 30673

American (AMR) AF: 0.792 AC: 8282 AN: 10460

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2102 AN: 2628

East Asian (EAS) AF: 0.998 AC: 3518 AN: 3525

South Asian (SAS) AF: 0.903 AC: 2370 AN: 2626

European-Finnish (FIN) AF: 0.824 AC: 4866 AN: 5904

Middle Eastern (MID) AF: 0.636 AC: 136 AN: 214

European-Non Finnish (NFE) AF: 0.796 AC: 42147 AN: 52955

Other (OTH) AF: 0.665 AC: 1018 AN: 1530

Alfa AF: 0.726 Hom.: 26054

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.53
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs1337082; hg19: chrX-66984015;