chrX-84961969-C-G

Variant names:

• chrX-84961969-C-G
• rs485709

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 0.76 (23015 hom., 24598 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.763 AC: 83764 AN: 109724 Hom.: 23016 Cov.: 22

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.774

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: 0.764 AC: 83821 AN: 109773 Hom.: 23015 Cov.: 22 AF XY: 0.767 AC XY: 24598 AN XY: 32091

African (AFR) AF: 0.922 AC: 27973 AN: 30324

American (AMR) AF: 0.741 AC: 7580 AN: 10224

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 1990 AN: 2627

East Asian (EAS) AF: 0.673 AC: 2340 AN: 3476

South Asian (SAS) AF: 0.851 AC: 2183 AN: 2566

European-Finnish (FIN) AF: 0.739 AC: 4198 AN: 5680

Middle Eastern (MID) AF: 0.821 AC: 174 AN: 212

European-Non Finnish (NFE) AF: 0.683 AC: 35846 AN: 52514

Other (OTH) AF: 0.772 AC: 1149 AN: 1488

Alfa AF: 0.712 Hom.: 5468

Bravo AF: 0.768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.42
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs485709; hg19: chrX-84216975;