X-146847808-T-C

Variant names:

• chrX-146847808-T-C
• rs4824284

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.758 AC: 82856 AN: 109261 Hom.: 22535 Cov.: 22

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

African (AFR) AF: 0.795 AC: 23896 AN: 30060

American (AMR) AF: 0.749 AC: 7606 AN: 10154

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2083 AN: 2615

East Asian (EAS) AF: 0.834 AC: 2853 AN: 3421

South Asian (SAS) AF: 0.819 AC: 2065 AN: 2520

European-Finnish (FIN) AF: 0.714 AC: 4057 AN: 5685

Middle Eastern (MID) AF: 0.676 AC: 142 AN: 210

European-Non Finnish (NFE) AF: 0.735 AC: 38560 AN: 52489

Other (OTH) AF: 0.756 AC: 1122 AN: 1485

Alfa AF: 0.744 Hom.: 58139

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.24
PhyloP100		-0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4824284;

hg19: chrX-145929326;