rs6525667

chrX-146286508-G-AchrX-146286508-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 0.33 in 110,266 control chromosomes in the GnomAD database, including 4,735 homozygotes. There are 10,703 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 0.33 (4735 hom., 10703 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 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: 0.330 AC: 36362 AN: 110216 Hom.: 4728 Cov.: 23 AF XY: 0.328 AC XY: 10679 AN XY: 32534

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.330 AC: 36400 AN: 110266 Hom.: 4735 Cov.: 23 AF XY: 0.328 AC XY: 10703 AN XY: 32594

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.347

Alfa AF: 0.362 Hom.: 17101

Bravo AF: 0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.0
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6525667; hg19: chrX-145368026;