XR_938423.3:n.81+6449A>T

Variant names:

• chrX-67778361-T-A
• rs945048
• XR_938423.3:n.81+6449A>T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The XR_938423.3(NXTAR):​n.81+6449A>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 (30664 hom., 27159 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: NXTAR XR_938423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXTAR	XR_938423.3	n.81+6449A>T		intron_variant	Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.868 AC: 94363 AN: 108658 Hom.: 30674 Cov.: 21 AF XY: 0.875 AC XY: 27130 AN XY: 31014

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: 0.998

Gnomad OTH AF: 0.906

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: 94376 AN: 108709 Hom.: 30664 Cov.: 21 AF XY: 0.874 AC XY: 27159 AN XY: 31075

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.997

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.907

Alfa AF: 0.874 Hom.: 3290

Bravo AF: 0.851

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs945048; hg19: chrX-66998203;