X-147486683-A-G

Variant names:

• chrX-147486683-A-G
• rs560689

Variant summary

Our verdict is Likely benign. Variant got -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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.782 AC: 86433 AN: 110488 Hom.: 23978 Cov.: 22 AF XY: 0.780 AC XY: 25504 AN XY: 32698

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

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.769

Alfa AF: 0.797 Hom.: 8752

Bravo AF: 0.771

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs560689; hg19: chrX-146568201;