X-89583107-C-A

Variant names:

• chrX-89583107-C-A
• rs223679

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 0.79 (25092 hom., 17961 hem., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• 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=-0.96).

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: 0.790 AC: 79833 AN: 100993 Hom.: 25097 Cov.: 17

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.801

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: 0.790 AC: 79860 AN: 101034 Hom.: 25092 Cov.: 17 AF XY: 0.735 AC XY: 17961 AN XY: 24426

African (AFR) AF: 0.801 AC: 22108 AN: 27601

American (AMR) AF: 0.728 AC: 6664 AN: 9150

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 1968 AN: 2490

East Asian (EAS) AF: 0.701 AC: 2186 AN: 3117

South Asian (SAS) AF: 0.565 AC: 1207 AN: 2136

European-Finnish (FIN) AF: 0.768 AC: 3661 AN: 4765

Middle Eastern (MID) AF: 0.834 AC: 166 AN: 199

European-Non Finnish (NFE) AF: 0.813 AC: 40350 AN: 49623

Other (OTH) AF: 0.800 AC: 1056 AN: 1320

Alfa AF: 0.817 Hom.: 6073

Bravo AF: 0.809

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.79
DANN	Benign	0.75
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: rs223679; hg19: chrX-88838106;