rs12012620

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 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: 0.231 AC: 25461 AN: 110449 Hom.: 2556 Cov.: 22

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

African (AFR) AF: 0.363 AC: 10979 AN: 30263

American (AMR) AF: 0.153 AC: 1591 AN: 10404

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 524 AN: 2627

East Asian (EAS) AF: 0.00142 AC: 5 AN: 3529

South Asian (SAS) AF: 0.0883 AC: 227 AN: 2572

European-Finnish (FIN) AF: 0.165 AC: 971 AN: 5871

Middle Eastern (MID) AF: 0.315 AC: 67 AN: 213

European-Non Finnish (NFE) AF: 0.202 AC: 10668 AN: 52830

Other (OTH) AF: 0.236 AC: 359 AN: 1519

Alfa AF: 0.204 Hom.: 3264

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs12012620; hg19: chrX-66971020;