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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXTAR	XR_938423.3	n.82-4919A>G		intron_variant	Intron 1 of 4

Ensembl

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

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 v4.3

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;