rs7055763

Variant names:

• chrX-80014183-G-A
• rs7055763

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.109 in 109,552 control chromosomes in the GnomAD database, including 835 homozygotes. There are 3,546 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.11 (835 hom., 3546 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant X-80014183-G-A is Benign according to our data. Variant chrX-80014183-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 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: 0.108 AC: 11863 AN: 109506 Hom.: 834 Cov.: 22 AF XY: 0.111 AC XY: 3526 AN XY: 31908

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0586

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0466

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.109 AC: 11891 AN: 109552 Hom.: 835 Cov.: 22 AF XY: 0.111 AC XY: 3546 AN XY: 31964

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0870

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0349

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0744 Hom.: 353

Bravo AF: 0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7055763; hg19: chrX-79269682;