rs12012620

Variant names:

• chrX-67751178-G-A
• rs12012620
• XR_938423.3:n.214+48C>T

Variant summary

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

The XR_938423.3(NXTAR):​n.214+48C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 110,501 control chromosomes in the GnomAD database, including 2,560 homozygotes. There are 6,892 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 (2560 hom., 6892 hem., cov: 22)
• Consequence: NXTAR XR_938423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXTAR	XR_938423.3	n.214+48C>T		intron_variant	Intron 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.231 AC: 25461 AN: 110449 Hom.: 2556 Cov.: 22 AF XY: 0.210 AC XY: 6884 AN XY: 32725

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.00141

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.231 AC: 25475 AN: 110501 Hom.: 2560 Cov.: 22 AF XY: 0.210 AC XY: 6892 AN XY: 32787

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.00142

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.236

Alfa AF: 0.210 Hom.: 1809

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12012620; hg19: chrX-66971020;