X-76654849-C-T

Variant names:

• chrX-76654849-C-T
• rs2189394
• ENST00000411327.1:n.*160G>A

Variant summary

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

The ENST00000411327.1(RNA5SP508):​n.*160G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 109,769 control chromosomes in the GnomAD database, including 16,480 homozygotes. There are 18,723 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 0.58 (16480 hom., 18723 hem., cov: 23)
• Consequence: RNA5SP508 ENST00000411327.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

Genes affected

RNA5SP508 (HGNC:43408): (RNA, 5S ribosomal pseudogene 508)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNA5SP508	ENST00000411327.1	n.*160G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.585 AC: 64170 AN: 109719 Hom.: 16492 Cov.: 23 AF XY: 0.583 AC XY: 18701 AN XY: 32065

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.585 AC: 64168 AN: 109769 Hom.: 16480 Cov.: 23 AF XY: 0.583 AC XY: 18723 AN XY: 32125

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.623

Alfa AF: 0.725 Hom.: 16323

Bravo AF: 0.549

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2189394; hg19: chrX-75875250;