rs5908575

chrX-143166523-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.383 AC: 42265 AN: 110355 Hom.: 7377 Cov.: 23 AF XY: 0.370 AC XY: 12089 AN XY: 32641

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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.363

Alfa AF: 0.329 Hom.: 2251

Bravo AF: 0.390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.71
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5908575; hg19: chrX-142254309;