X-84669362-A-G

Variant names:

• chrX-84669362-A-G
• rs5922075

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 0.74 (21868 hom., 24569 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• 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=-0.82).

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: 0.735 AC: 81276 AN: 110515 Hom.: 21879 Cov.: 23

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.784

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.787

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: 0.735 AC: 81300 AN: 110568 Hom.: 21868 Cov.: 23 AF XY: 0.748 AC XY: 24569 AN XY: 32834

African (AFR) AF: 0.463 AC: 14066 AN: 30385

American (AMR) AF: 0.866 AC: 9020 AN: 10411

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2250 AN: 2628

East Asian (EAS) AF: 0.984 AC: 3419 AN: 3473

South Asian (SAS) AF: 0.871 AC: 2244 AN: 2577

European-Finnish (FIN) AF: 0.858 AC: 5063 AN: 5898

Middle Eastern (MID) AF: 0.781 AC: 164 AN: 210

European-Non Finnish (NFE) AF: 0.823 AC: 43452 AN: 52816

Other (OTH) AF: 0.785 AC: 1178 AN: 1500

Alfa AF: 0.786 Hom.: 85707

Bravo AF: 0.727

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.37
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs5922075; hg19: chrX-83924370;