X-146847808-T-C

Variant names:

• chrX-146847808-T-C
• rs4824284

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 0.76 (22537 hom., 23886 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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: 0.758 AC: 82856 AN: 109261 Hom.: 22535 Cov.: 22 AF XY: 0.754 AC XY: 23847 AN XY: 31635

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.752

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: 0.758 AC: 82895 AN: 109312 Hom.: 22537 Cov.: 22 AF XY: 0.754 AC XY: 23886 AN XY: 31696

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.756

Alfa AF: 0.745 Hom.: 42858

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4824284; hg19: chrX-145929326;