rs5908575

Variant names:

• chrX-143166523-G-C
• rs5908575

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.383 in 110,405 control chromosomes in the GnomAD database, including 7,379 homozygotes. There are 12,130 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 0.38 (7379 hom., 12130 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.383 AC: 42265 AN: 110355 Hom.: 7377 Cov.: 23

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.383 AC: 42309 AN: 110405 Hom.: 7379 Cov.: 23 AF XY: 0.371 AC XY: 12130 AN XY: 32701

African (AFR) AF: 0.696 AC: 21106 AN: 30336

American (AMR) AF: 0.232 AC: 2407 AN: 10391

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 660 AN: 2651

East Asian (EAS) AF: 0.242 AC: 845 AN: 3490

South Asian (SAS) AF: 0.289 AC: 768 AN: 2653

European-Finnish (FIN) AF: 0.344 AC: 1987 AN: 5778

Middle Eastern (MID) AF: 0.330 AC: 70 AN: 212

European-Non Finnish (NFE) AF: 0.262 AC: 13796 AN: 52708

Other (OTH) AF: 0.363 AC: 545 AN: 1503

Alfa AF: 0.329 Hom.: 2251

Bravo AF: 0.390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.40
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs5908575; hg19: chrX-142254309;