chrX-89582521-G-A

Position:

• chrX-89582521-G-A

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 0.72 (20997 hom., 7581 hem., cov: 13)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.00 AC: 61412 AN: 84988 Hom.: 21004 Cov.: 13 AF XY: 0.501 AC XY: 7553 AN XY: 15066 FAILED QC

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.721

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: AS_VQSR;InbreedingCoeff AF: 0.722 AC: 61424 AN: 85023 Hom.: 20997 Cov.: 13 AF XY: 0.501 AC XY: 7581 AN XY: 15117

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.722

Alfa AF: 0.796 Hom.: 5839

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223678; hg19: chrX-88837520;