rs945052

Variant names:

• chrX-67766885-T-C
• rs945052
• XR_938423.3:n.82-4919A>G

Your query was ambiguous. Multiple possible variants found:

• chrX-67766885-T-C
• chrX-67766885-T-G

Variant summary

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

The XR_938423.3(NXTAR):​n.82-4919A>G 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 0.86 (30506 hom., 28308 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: NXTAR XR_938423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 2 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: 0.863 AC: 95232 AN: 110347 Hom.: 30517 Cov.: 22

Gnomad AFR AF: 0.525

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.962

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: 0.863 AC: 95243 AN: 110396 Hom.: 30506 Cov.: 22 AF XY: 0.868 AC XY: 28308 AN XY: 32624

African (AFR) AF: 0.525 AC: 15941 AN: 30356

American (AMR) AF: 0.949 AC: 9788 AN: 10310

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 2630 AN: 2632

East Asian (EAS) AF: 1.00 AC: 3490 AN: 3490

South Asian (SAS) AF: 0.997 AC: 2517 AN: 2525

European-Finnish (FIN) AF: 1.00 AC: 5799 AN: 5799

Middle Eastern (MID) AF: 0.958 AC: 205 AN: 214

European-Non Finnish (NFE) AF: 0.999 AC: 52818 AN: 52878

Other (OTH) AF: 0.909 AC: 1370 AN: 1507

Alfa AF: 0.914 Hom.: 9398

Bravo AF: 0.845

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.47
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs945052; hg19: chrX-66986727;