X-83699482-C-T

Variant names:

• chrX-83699482-C-T
• rs5968205

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 0.78 (23853 hom., 25112 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

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: 0.781 AC: 85712 AN: 109725 Hom.: 23870 Cov.: 22

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.794

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: 0.781 AC: 85731 AN: 109778 Hom.: 23853 Cov.: 22 AF XY: 0.781 AC XY: 25112 AN XY: 32146

African (AFR) AF: 0.664 AC: 20108 AN: 30265

American (AMR) AF: 0.817 AC: 8345 AN: 10215

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2137 AN: 2625

East Asian (EAS) AF: 0.710 AC: 2445 AN: 3445

South Asian (SAS) AF: 0.704 AC: 1823 AN: 2588

European-Finnish (FIN) AF: 0.807 AC: 4592 AN: 5691

Middle Eastern (MID) AF: 0.734 AC: 157 AN: 214

European-Non Finnish (NFE) AF: 0.845 AC: 44423 AN: 52571

Other (OTH) AF: 0.784 AC: 1171 AN: 1494

Alfa AF: 0.815 Hom.: 84461

Bravo AF: 0.775

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.73
DANN	Benign	0.26
PhyloP100		-0.92

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: rs5968205; hg19: chrX-82954490;