X-66052274-A-G

Variant names:

• chrX-66052274-A-G
• rs670546

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 0.79 (24942 hom., 26315 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.791 AC: 87624 AN: 110724 Hom.: 24949 Cov.: 23

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.829

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: 0.791 AC: 87633 AN: 110774 Hom.: 24942 Cov.: 23 AF XY: 0.797 AC XY: 26315 AN XY: 33006

African (AFR) AF: 0.574 AC: 17458 AN: 30434

American (AMR) AF: 0.825 AC: 8623 AN: 10454

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 2366 AN: 2634

East Asian (EAS) AF: 0.999 AC: 3543 AN: 3545

South Asian (SAS) AF: 0.918 AC: 2375 AN: 2587

European-Finnish (FIN) AF: 0.880 AC: 5130 AN: 5830

Middle Eastern (MID) AF: 0.852 AC: 184 AN: 216

European-Non Finnish (NFE) AF: 0.872 AC: 46125 AN: 52899

Other (OTH) AF: 0.829 AC: 1244 AN: 1500

Alfa AF: 0.839 Hom.: 94086

Bravo AF: 0.779

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.75

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs670546; hg19: chrX-65272116;