rs945048

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrX-67778361-T-A
• chrX-67778361-T-C
• chrX-67778361-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.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
• Publications: 1 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=-0.96).

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: 0.868 AC: 94363 AN: 108658 Hom.: 30674 Cov.: 21

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

African (AFR) AF: 0.543 AC: 16181 AN: 29783

American (AMR) AF: 0.951 AC: 9567 AN: 10056

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 2619 AN: 2621

East Asian (EAS) AF: 1.00 AC: 3460 AN: 3460

South Asian (SAS) AF: 0.997 AC: 2377 AN: 2385

European-Finnish (FIN) AF: 1.00 AC: 5447 AN: 5447

Middle Eastern (MID) AF: 0.963 AC: 206 AN: 214

European-Non Finnish (NFE) AF: 0.998 AC: 52516 AN: 52604

Other (OTH) AF: 0.907 AC: 1326 AN: 1462

Alfa AF: 0.874 Hom.: 3290

Bravo AF: 0.851

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.30
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs945048; hg19: chrX-66998203;