X-121445819-C-G

Variant names:

• chrX-121445819-C-G
• rs4825770

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 0.81 (25600 hom., 27369 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• 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=-0.97).

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: 0.813 AC: 90284 AN: 110990 Hom.: 25598 Cov.: 23

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.808

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: 0.814 AC: 90332 AN: 111040 Hom.: 25600 Cov.: 23 AF XY: 0.823 AC XY: 27369 AN XY: 33252

African (AFR) AF: 0.797 AC: 24400 AN: 30634

American (AMR) AF: 0.881 AC: 9165 AN: 10399

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 1827 AN: 2638

East Asian (EAS) AF: 0.999 AC: 3526 AN: 3531

South Asian (SAS) AF: 0.935 AC: 2453 AN: 2624

European-Finnish (FIN) AF: 0.830 AC: 4867 AN: 5866

Middle Eastern (MID) AF: 0.612 AC: 131 AN: 214

European-Non Finnish (NFE) AF: 0.795 AC: 42099 AN: 52925

Other (OTH) AF: 0.810 AC: 1237 AN: 1527

Alfa AF: 0.788 Hom.: 6250

Bravo AF: 0.817

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.72
DANN	Benign	0.48
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4825770; hg19: chrX-120579673;