rs3788766

Variant names:

• chrX-116435671-G-A
• rs3788766

Variant summary

Our verdict is Likely benign. Variant got -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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.543 AC: 60182 AN: 110748 Hom.: 12530 Cov.: 23 AF XY: 0.545 AC XY: 17980 AN XY: 32980

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

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.570

Alfa AF: 0.628 Hom.: 59011

Bravo AF: 0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3788766; hg19: chrX-115566839;