chrX-89544271-T-G

Variant names:

• chrX-89544271-T-G
• rs223792

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 0.77 (23836 hom., 13395 hem., cov: 15)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• 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=-1.04).

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: 0.771 AC: 72760 AN: 94345 Hom.: 23843 Cov.: 15

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.773

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: 0.771 AC: 72746 AN: 94362 Hom.: 23836 Cov.: 15 AF XY: 0.667 AC XY: 13395 AN XY: 20078

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.751 AC: 19307 AN: 25706

American (AMR) AF: 0.705 AC: 5804 AN: 8238

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 1886 AN: 2361

East Asian (EAS) AF: 0.727 AC: 2200 AN: 3026

South Asian (SAS) AF: 0.536 AC: 1053 AN: 1964

European-Finnish (FIN) AF: 0.729 AC: 2848 AN: 3905

Middle Eastern (MID) AF: 0.836 AC: 158 AN: 189

European-Non Finnish (NFE) AF: 0.808 AC: 38064 AN: 47132

Other (OTH) AF: 0.772 AC: 939 AN: 1217

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.663 Hom.: 2043

Bravo AF: 0.800

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.53
PhyloP100		-2.0

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: rs223792;

hg19: chrX-88799270;