X-147486683-A-G

Variant names:

• chrX-147486683-A-G
• rs560689

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 0.78 (23981 hom., 25531 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• 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=-0.88).

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: 0.782 AC: 86433 AN: 110488 Hom.: 23978 Cov.: 22

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.770

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: 0.782 AC: 86459 AN: 110537 Hom.: 23981 Cov.: 22 AF XY: 0.779 AC XY: 25531 AN XY: 32757

African (AFR) AF: 0.700 AC: 21286 AN: 30418

American (AMR) AF: 0.732 AC: 7565 AN: 10341

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 1974 AN: 2637

East Asian (EAS) AF: 0.876 AC: 3042 AN: 3474

South Asian (SAS) AF: 0.730 AC: 1897 AN: 2598

European-Finnish (FIN) AF: 0.873 AC: 5093 AN: 5834

Middle Eastern (MID) AF: 0.842 AC: 181 AN: 215

European-Non Finnish (NFE) AF: 0.826 AC: 43615 AN: 52833

Other (OTH) AF: 0.769 AC: 1159 AN: 1507

Alfa AF: 0.769 Hom.: 20813

Bravo AF: 0.771

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.54
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs560689; hg19: chrX-146568201;