rs6525299

Variant names:

• chrX-69403207-G-A
• rs6525299

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 0.0992 in 109,169 control chromosomes in the GnomAD database, including 472 homozygotes. There are 3,075 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 0.099 (472 hom., 3075 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0992 AC: 10820 AN: 109126 Hom.: 472 Cov.: 22

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0558

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0791

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0213

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0786

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

GnomAD4 genome AF: 0.0992 AC: 10825 AN: 109169 Hom.: 472 Cov.: 22 AF XY: 0.0970 AC XY: 3075 AN XY: 31687

African (AFR) AF: 0.0485 AC: 1445 AN: 29823

American (AMR) AF: 0.0526 AC: 540 AN: 10258

Ashkenazi Jewish (ASJ) AF: 0.0558 AC: 146 AN: 2615

East Asian (EAS) AF: 0.121 AC: 416 AN: 3433

South Asian (SAS) AF: 0.0794 AC: 195 AN: 2457

European-Finnish (FIN) AF: 0.200 AC: 1107 AN: 5543

Middle Eastern (MID) AF: 0.0234 AC: 5 AN: 214

European-Non Finnish (NFE) AF: 0.126 AC: 6637 AN: 52674

Other (OTH) AF: 0.0790 AC: 117 AN: 1481

Alfa AF: 0.109 Hom.: 6754

Bravo AF: 0.0865

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.54
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs6525299; hg19: chrX-68623050;