rs5919324

Positions:

• chrX-67210798-G-A
• chrX-67210798-G-C

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 0.65 (20380 hom., 21350 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67210798G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.652 AC: 71694 AN: 109901 Hom.: 20390 Cov.: 22 AF XY: 0.663 AC XY: 21338 AN XY: 32173

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.695

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: 0.652 AC: 71680 AN: 109954 Hom.: 20380 Cov.: 22 AF XY: 0.662 AC XY: 21350 AN XY: 32236

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.697

Alfa AF: 0.793 Hom.: 12294

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.1
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: rs5919324; hg19: chrX-66430640;