rs7055778

Variant names:

• chrX-830669-G-A
• rs7055778

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.465 AC: 19170 AN: 41220

American (AMR) AF: 0.700 AC: 10631 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2182 AN: 3462

East Asian (EAS) AF: 0.396 AC: 2029 AN: 5126

South Asian (SAS) AF: 0.661 AC: 3171 AN: 4794

European-Finnish (FIN) AF: 0.677 AC: 7040 AN: 10392

Middle Eastern (MID) AF: 0.600 AC: 174 AN: 290

European-Non Finnish (NFE) AF: 0.688 AC: 46709 AN: 67862

Other (OTH) AF: 0.620 AC: 1301 AN: 2100

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7055778; hg19: chrX-791404;