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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXTAR	XR_938423.3	n.82-2207C>T		intron_variant	Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.627 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 v4.3

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;