X-71206265-A-T

Variant names:

• chrX-71206265-A-T
• rs9698122

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 0.60 (15367 hom., 18205 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

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: 0.603 AC: 64954 AN: 107650 Hom.: 15358 Cov.: 20

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.633

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: 0.604 AC: 65017 AN: 107700 Hom.: 15367 Cov.: 20 AF XY: 0.599 AC XY: 18205 AN XY: 30380

African (AFR) AF: 0.837 AC: 24767 AN: 29573

American (AMR) AF: 0.635 AC: 6329 AN: 9962

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 1792 AN: 2600

East Asian (EAS) AF: 0.750 AC: 2531 AN: 3374

South Asian (SAS) AF: 0.607 AC: 1521 AN: 2506

European-Finnish (FIN) AF: 0.393 AC: 2095 AN: 5330

Middle Eastern (MID) AF: 0.689 AC: 144 AN: 209

European-Non Finnish (NFE) AF: 0.470 AC: 24477 AN: 52048

Other (OTH) AF: 0.639 AC: 925 AN: 1448

Alfa AF: 0.523 Hom.: 3138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.1
DANN	Benign	0.10
PhyloP100		-2.8

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: rs9698122;

hg19: chrX-70426115;