rs3788766

Variant names:

• chrX-116435671-G-A
• rs3788766

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 0.54 (12527 hom., 17983 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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: 0.543 AC: 60182 AN: 110748 Hom.: 12530 Cov.: 23

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.569

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: 0.543 AC: 60176 AN: 110802 Hom.: 12527 Cov.: 23 AF XY: 0.544 AC XY: 17983 AN XY: 33044

African (AFR) AF: 0.289 AC: 8843 AN: 30588

American (AMR) AF: 0.585 AC: 6106 AN: 10431

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2028 AN: 2633

East Asian (EAS) AF: 0.747 AC: 2578 AN: 3450

South Asian (SAS) AF: 0.660 AC: 1728 AN: 2620

European-Finnish (FIN) AF: 0.684 AC: 4000 AN: 5849

Middle Eastern (MID) AF: 0.670 AC: 142 AN: 212

European-Non Finnish (NFE) AF: 0.632 AC: 33370 AN: 52835

Other (OTH) AF: 0.570 AC: 861 AN: 1511

Alfa AF: 0.600 Hom.: 76839

Bravo AF: 0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.64
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs3788766; hg19: chrX-115566839;