rs6646773

chrX-117088295-A-G

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 0.0835 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0834 AC: 9276 AN: 111181 Hom.: 556 Cov.: 23 AF XY: 0.0818 AC XY: 2731 AN XY: 33399

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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0186

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.00688

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0356 Hom.: 1069

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.8
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6646773; hg19: chrX-116222263;