X-66052730-C-T

Variant names:

• chrX-66052730-C-T
• rs668389

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 (24517 hom., 25484 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• 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=-0.99).

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: 0.783 AC: 86054 AN: 109833 Hom.: 24528 Cov.: 22

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.818

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: 0.783 AC: 86050 AN: 109873 Hom.: 24517 Cov.: 22 AF XY: 0.791 AC XY: 25484 AN XY: 32207

African (AFR) AF: 0.547 AC: 16503 AN: 30183

American (AMR) AF: 0.820 AC: 8407 AN: 10253

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 2352 AN: 2623

East Asian (EAS) AF: 0.999 AC: 3529 AN: 3531

South Asian (SAS) AF: 0.918 AC: 2411 AN: 2625

European-Finnish (FIN) AF: 0.881 AC: 4901 AN: 5566

Middle Eastern (MID) AF: 0.846 AC: 181 AN: 214

European-Non Finnish (NFE) AF: 0.872 AC: 45952 AN: 52701

Other (OTH) AF: 0.818 AC: 1229 AN: 1502

Alfa AF: 0.822 Hom.: 7030

Bravo AF: 0.770

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.13
PhyloP100		-1.0

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: rs668389;

hg19: chrX-65272572;