rs6525479

Variant names:

• chrX-71202153-C-T
• rs6525479

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 0.342 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.528 AC: 16020 AN: 30320

American (AMR) AF: 0.431 AC: 4444 AN: 10314

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 570 AN: 2644

East Asian (EAS) AF: 0.741 AC: 2554 AN: 3449

South Asian (SAS) AF: 0.464 AC: 1206 AN: 2597

European-Finnish (FIN) AF: 0.234 AC: 1373 AN: 5866

Middle Eastern (MID) AF: 0.156 AC: 33 AN: 212

European-Non Finnish (NFE) AF: 0.207 AC: 10947 AN: 52881

Other (OTH) AF: 0.330 AC: 495 AN: 1499

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6525479; hg19: chrX-70422003;