chrX-100014722-G-A

Variant names:

• chrX-100014722-G-A
• rs1381733

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 0.64 (16749 hom., 21060 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• 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: 0.638 AC: 70346 AN: 110211 Hom.: 16750 Cov.: 23

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.530

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.656

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: 0.638 AC: 70368 AN: 110264 Hom.: 16749 Cov.: 23 AF XY: 0.646 AC XY: 21060 AN XY: 32576

African (AFR) AF: 0.382 AC: 11603 AN: 30372

American (AMR) AF: 0.724 AC: 7475 AN: 10322

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 1642 AN: 2637

East Asian (EAS) AF: 0.999 AC: 3499 AN: 3504

South Asian (SAS) AF: 0.888 AC: 2261 AN: 2546

European-Finnish (FIN) AF: 0.746 AC: 4290 AN: 5752

Middle Eastern (MID) AF: 0.521 AC: 111 AN: 213

European-Non Finnish (NFE) AF: 0.718 AC: 37898 AN: 52755

Other (OTH) AF: 0.661 AC: 981 AN: 1485

Alfa AF: 0.710 Hom.: 22080

Bravo AF: 0.630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.70
PhyloP100		-0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1381733; hg19: chrX-99269720;