X-28213017-A-G

Variant names:

• chrX-28213017-A-G
• rs5926352

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 0.58 (13486 hom., 18863 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• 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=-0.84).

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: 0.582 AC: 63932 AN: 109905 Hom.: 13486 Cov.: 22

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.555

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.575

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: 0.582 AC: 63959 AN: 109956 Hom.: 13486 Cov.: 22 AF XY: 0.585 AC XY: 18863 AN XY: 32248

African (AFR) AF: 0.438 AC: 13283 AN: 30295

American (AMR) AF: 0.655 AC: 6763 AN: 10318

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1497 AN: 2628

East Asian (EAS) AF: 0.835 AC: 2854 AN: 3416

South Asian (SAS) AF: 0.556 AC: 1419 AN: 2554

European-Finnish (FIN) AF: 0.673 AC: 3836 AN: 5699

Middle Eastern (MID) AF: 0.540 AC: 116 AN: 215

European-Non Finnish (NFE) AF: 0.624 AC: 32833 AN: 52652

Other (OTH) AF: 0.579 AC: 870 AN: 1502

Alfa AF: 0.596 Hom.: 45943

Bravo AF: 0.583

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.81
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs5926352; hg19: chrX-28231134;