X-147956770-A-G

Variant names:

• chrX-147956770-A-G
• rs5904817

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 0.55 (12686 hom., 17861 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.549 AC: 60996 AN: 111063 Hom.: 12690 Cov.: 23

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.563

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: 0.549 AC: 61034 AN: 111117 Hom.: 12686 Cov.: 23 AF XY: 0.535 AC XY: 17861 AN XY: 33375

African (AFR) AF: 0.743 AC: 22638 AN: 30481

American (AMR) AF: 0.505 AC: 5310 AN: 10523

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1219 AN: 2636

East Asian (EAS) AF: 0.750 AC: 2601 AN: 3469

South Asian (SAS) AF: 0.463 AC: 1237 AN: 2671

European-Finnish (FIN) AF: 0.397 AC: 2376 AN: 5987

Middle Eastern (MID) AF: 0.540 AC: 114 AN: 211

European-Non Finnish (NFE) AF: 0.459 AC: 24274 AN: 52935

Other (OTH) AF: 0.567 AC: 868 AN: 1532

Alfa AF: 0.510 Hom.: 34090

Bravo AF: 0.573

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.53
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs5904817; hg19: chrX-147038290;