rs7055763

Positions:

• chrX-80014183-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;