X-78328090-G-T

Position:

• chrX-78328090-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 0.79 (24847 hom., 25011 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

Genes affected

(HGNC:):

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
		n.78328090G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.789 AC: 86665 AN: 109903 Hom.: 24855 Cov.: 22 AF XY: 0.777 AC XY: 24961 AN XY: 32131

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.738

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.762

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: 0.789 AC: 86701 AN: 109956 Hom.: 24847 Cov.: 22 AF XY: 0.777 AC XY: 25011 AN XY: 32194

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.758

Alfa AF: 0.716 Hom.: 7354

Bravo AF: 0.787

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2637204; hg19: chrX-77583587;