X-66117875-G-T

Variant names:

• chrX-66117875-G-T
• rs1359524

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 0.73 (22070 hom., 24232 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• 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: 0.726 AC: 80411 AN: 110721 Hom.: 22076 Cov.: 23

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.855

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.771

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: 0.726 AC: 80419 AN: 110775 Hom.: 22070 Cov.: 23 AF XY: 0.734 AC XY: 24232 AN XY: 33025

African (AFR) AF: 0.390 AC: 11897 AN: 30510

American (AMR) AF: 0.799 AC: 8269 AN: 10352

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2142 AN: 2631

East Asian (EAS) AF: 0.999 AC: 3529 AN: 3534

South Asian (SAS) AF: 0.903 AC: 2351 AN: 2603

European-Finnish (FIN) AF: 0.864 AC: 5012 AN: 5804

Middle Eastern (MID) AF: 0.845 AC: 180 AN: 213

European-Non Finnish (NFE) AF: 0.855 AC: 45280 AN: 52936

Other (OTH) AF: 0.772 AC: 1166 AN: 1511

Alfa AF: 0.761 Hom.: 8390

Bravo AF: 0.710

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.61
PhyloP100		-0.36

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: rs1359524; hg19: chrX-65337717;