rs7055778

Positions:

• chrX-830669-G-A

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 0.614 in 151,334 control chromosomes in the GnomAD database, including 29,577 homozygotes. There are 45,524 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 0.61 (29577 hom., 45524 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.689 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: 0.614 AC: 92907 AN: 151214 Hom.: 29550 Cov.: 29 AF XY: 0.616 AC XY: 45448 AN XY: 73726

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.614 AC: 92978 AN: 151334 Hom.: 29577 Cov.: 29 AF XY: 0.616 AC XY: 45524 AN XY: 73856

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.620

Bravo AF: 0.607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.084
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7055778; hg19: chrX-791404;