chrX-66117875-G-T

Position:

• chrX-66117875-G-T

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 0.73 (22070 hom., 24232 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.726 AC: 80411 AN: 110721 Hom.: 22076 Cov.: 23 AF XY: 0.735 AC XY: 24213 AN XY: 32961

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.855

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.771

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: 0.726 AC: 80419 AN: 110775 Hom.: 22070 Cov.: 23 AF XY: 0.734 AC XY: 24232 AN XY: 33025

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.772

Alfa AF: 0.761 Hom.: 8390

Bravo AF: 0.710

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1359524; hg19: chrX-65337717;