X-71204813-C-A

Variant names:

• chrX-71204813-C-A
• rs7884258

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.60 (14973 hom., 17430 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.16
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.597 AC: 63682 AN: 106758 Hom.: 14963 Cov.: 20

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.681

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.626

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.597 AC: 63744 AN: 106811 Hom.: 14973 Cov.: 20 AF XY: 0.592 AC XY: 17430 AN XY: 29429

African (AFR) AF: 0.823 AC: 24138 AN: 29345

American (AMR) AF: 0.631 AC: 6173 AN: 9782

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 1754 AN: 2582

East Asian (EAS) AF: 0.753 AC: 2524 AN: 3354

South Asian (SAS) AF: 0.608 AC: 1460 AN: 2400

European-Finnish (FIN) AF: 0.387 AC: 2041 AN: 5270

Middle Eastern (MID) AF: 0.697 AC: 145 AN: 208

European-Non Finnish (NFE) AF: 0.467 AC: 24162 AN: 51771

Other (OTH) AF: 0.633 AC: 918 AN: 1451

Alfa AF: 0.294 Hom.: 1170

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.26
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs7884258; hg19: chrX-70424663;