X-100527829-T-G

Position:

• chrX-100527829-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.444 in 109,347 control chromosomes in the GnomAD database, including 8,378 homozygotes. There are 13,659 hemizygotes in GnomAD. 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 0.44 (8378 hom., 13659 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100527829T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.443 AC: 48468 AN: 109292 Hom.: 8373 Cov.: 22 AF XY: 0.430 AC XY: 13609 AN XY: 31620

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.394

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.444 AC: 48524 AN: 109347 Hom.: 8378 Cov.: 22 AF XY: 0.431 AC XY: 13659 AN XY: 31685

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.397

Alfa AF: 0.394 Hom.: 36829

Bravo AF: 0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5921594; hg19: chrX-99782826;