rs7055778

Variant names:

• chrX-830669-G-A
• rs7055778

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;