X-84961903-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 0.74 (21155 hom., 24085 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd at 21158 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: 0.737 AC: 81118 AN: 110027 Hom.: 21158 Cov.: 22 AF XY: 0.744 AC XY: 24031 AN XY: 32311

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.749

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: 0.737 AC: 81165 AN: 110079 Hom.: 21155 Cov.: 22 AF XY: 0.744 AC XY: 24085 AN XY: 32373

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.748

Alfa AF: 0.709 Hom.: 5712

Bravo AF: 0.738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.4
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4828313; hg19: chrX-84216909; COSMIC: COSV53902959;