X-67779856-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.226 AC: 24863 AN: 110040 Hom.: 2450 Cov.: 22

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

African (AFR) AF: 0.349 AC: 10497 AN: 30063

American (AMR) AF: 0.150 AC: 1560 AN: 10372

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 529 AN: 2629

East Asian (EAS) AF: 0.00201 AC: 7 AN: 3488

South Asian (SAS) AF: 0.0875 AC: 224 AN: 2559

European-Finnish (FIN) AF: 0.163 AC: 953 AN: 5831

Middle Eastern (MID) AF: 0.308 AC: 65 AN: 211

European-Non Finnish (NFE) AF: 0.201 AC: 10615 AN: 52754

Other (OTH) AF: 0.228 AC: 343 AN: 1505

Alfa AF: 0.201 Hom.: 3014

Bravo AF: 0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs945050; hg19: chrX-66999698;