X-76654849-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411327.1. You can select a different transcript below to see updated ACMG assignments.

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
	RNA5SP508	ENST00000411327.1	TSL:6	n.*160G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.585 AC: 64170 AN: 109719 Hom.: 16492 Cov.: 23

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

African (AFR) AF: 0.172 AC: 5213 AN: 30347

American (AMR) AF: 0.604 AC: 6159 AN: 10200

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2119 AN: 2621

East Asian (EAS) AF: 0.206 AC: 711 AN: 3456

South Asian (SAS) AF: 0.658 AC: 1687 AN: 2563

European-Finnish (FIN) AF: 0.782 AC: 4420 AN: 5650

Middle Eastern (MID) AF: 0.751 AC: 163 AN: 217

European-Non Finnish (NFE) AF: 0.802 AC: 42148 AN: 52554

Other (OTH) AF: 0.623 AC: 924 AN: 1482

Alfa AF: 0.688 Hom.: 24881

Bravo AF: 0.549

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2189394;

hg19: chrX-75875250;