X-83699482-C-T

Position:

• chrX-83699482-C-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 0.78 (23853 hom., 25112 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.83699482C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.781 AC: 85712 AN: 109725 Hom.: 23870 Cov.: 22 AF XY: 0.781 AC XY: 25060 AN XY: 32083

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.794

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: 0.781 AC: 85731 AN: 109778 Hom.: 23853 Cov.: 22 AF XY: 0.781 AC XY: 25112 AN XY: 32146

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.784

Alfa AF: 0.828 Hom.: 69431

Bravo AF: 0.775

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.73
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5968205; hg19: chrX-82954490;