X-99197876-A-G

Position:

• chrX-99197876-A-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 0.276 in 106,960 control chromosomes in the GnomAD database, including 5,770 homozygotes. There are 7,746 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 0.28 (5770 hom., 7746 hem., cov: 21)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.99197876A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.275 AC: 29431 AN: 106938 Hom.: 5765 Cov.: 21 AF XY: 0.258 AC XY: 7710 AN XY: 29860

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.276 AC: 29481 AN: 106960 Hom.: 5770 Cov.: 21 AF XY: 0.259 AC XY: 7746 AN XY: 29894

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0922

Gnomad4 SAS AF: 0.0948

Gnomad4 FIN AF: 0.0889

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.233

Alfa AF: 0.112 Hom.: 2325

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs226711; hg19: chrX-98452874;