X-67778361-T-A

Variant names:

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

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).

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

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 v4.3

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;