X-69585474-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.69 (19852 hom., 22024 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BS2: High Homozygotes in GnomAd at 19843 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.689 AC: 75689 AN: 109927 Hom.: 19843 Cov.: 22 AF XY: 0.682 AC XY: 21970 AN XY: 32193

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.653

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: 0.689 AC: 75753 AN: 109971 Hom.: 19852 Cov.: 22 AF XY: 0.683 AC XY: 22024 AN XY: 32247

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.658

Alfa AF: 0.576 Hom.: 47879

Bravo AF: 0.714

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.5
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4844096; hg19: chrX-68805318;