X-71206075-C-T

Position:

• chrX-71206075-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 0.59 (15000 hom., 17163 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.71206075C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 63447 AN: 106924 Hom.: 14991 Cov.: 20 AF XY: 0.581 AC XY: 17111 AN XY: 29452

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.624

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: 0.594 AC: 63506 AN: 106974 Hom.: 15000 Cov.: 20 AF XY: 0.582 AC XY: 17163 AN XY: 29514

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.629

Alfa AF: 0.525 Hom.: 3741

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35328964; hg19: chrX-70425925;