rs6525479

Variant names:

• chrX-71202153-C-T
• rs6525479

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 0.342 in 110,454 control chromosomes in the GnomAD database, including 5,683 homozygotes. There are 11,173 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 0.34 (5683 hom., 11173 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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

Frequencies

GnomAD3 genomes AF: 0.342 AC: 37708 AN: 110397 Hom.: 5679 Cov.: 22 AF XY: 0.341 AC XY: 11141 AN XY: 32669

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.342 AC: 37746 AN: 110454 Hom.: 5683 Cov.: 22 AF XY: 0.341 AC XY: 11173 AN XY: 32736

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.330

Alfa AF: 0.288 Hom.: 1855

Bravo AF: 0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6525479; hg19: chrX-70422003;