X-117088295-A-G

Variant names:

• chrX-117088295-A-G
• rs6646773

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 0.0835 in 111,229 control chromosomes in the GnomAD database, including 558 homozygotes. There are 2,745 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 0.084 (558 hom., 2745 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0834 AC: 9276 AN: 111181 Hom.: 556 Cov.: 23

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0186

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.00688

Gnomad MID AF: 0.0847

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0835 AC: 9291 AN: 111229 Hom.: 558 Cov.: 23 AF XY: 0.0820 AC XY: 2745 AN XY: 33457

African (AFR) AF: 0.162 AC: 4947 AN: 30565

American (AMR) AF: 0.128 AC: 1334 AN: 10452

Ashkenazi Jewish (ASJ) AF: 0.0186 AC: 49 AN: 2638

East Asian (EAS) AF: 0.325 AC: 1128 AN: 3473

South Asian (SAS) AF: 0.263 AC: 693 AN: 2639

European-Finnish (FIN) AF: 0.00688 AC: 41 AN: 5961

Middle Eastern (MID) AF: 0.0837 AC: 18 AN: 215

European-Non Finnish (NFE) AF: 0.0174 AC: 926 AN: 53077

Other (OTH) AF: 0.101 AC: 154 AN: 1522

Alfa AF: 0.0556 Hom.: 2364

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6646773; hg19: chrX-116222263;