X-67779856-T-C

Variant names:

• chrX-67779856-T-C
• rs945050
• XR_938423.3:n.81+4954A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_938423.3(NXTAR):​n.81+4954A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 110,092 control chromosomes in the GnomAD database, including 2,454 homozygotes. There are 6,599 hemizygotes in GnomAD. 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 0.23 (2454 hom., 6599 hem., cov: 22)
• Consequence: NXTAR XR_938423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.894

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXTAR	XR_938423.3	n.81+4954A>G		intron_variant	Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.226 AC: 24863 AN: 110040 Hom.: 2450 Cov.: 22 AF XY: 0.204 AC XY: 6591 AN XY: 32344

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.00200

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.231

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.226 AC: 24877 AN: 110092 Hom.: 2454 Cov.: 22 AF XY: 0.204 AC XY: 6599 AN XY: 32406

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.00201

Gnomad4 SAS AF: 0.0875

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.228

Alfa AF: 0.206 Hom.: 1559

Bravo AF: 0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs945050; hg19: chrX-66999698;