rs938059

chrX-67116885-C-AchrX-67116885-C-GchrX-67116885-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.66 (20461 hom., 21450 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High Homozygotes in GnomAd at 20468 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.658 AC: 72231 AN: 109841 Hom.: 20468 Cov.: 22 AF XY: 0.668 AC XY: 21438 AN XY: 32083

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.698

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: 0.657 AC: 72223 AN: 109892 Hom.: 20461 Cov.: 22 AF XY: 0.667 AC XY: 21450 AN XY: 32144

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.918

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.700

Alfa AF: 0.818 Hom.: 28903

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.9
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs938059; hg19: chrX-66336727;