X-107355477-A-G

Position:

• chrX-107355477-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 0.332 in 110,632 control chromosomes in the GnomAD database, including 5,731 homozygotes. There are 10,702 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 0.33 (5731 hom., 10702 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.107355477A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 36679 AN: 110580 Hom.: 5729 Cov.: 22 AF XY: 0.325 AC XY: 10670 AN XY: 32852

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.332 AC: 36709 AN: 110632 Hom.: 5731 Cov.: 22 AF XY: 0.325 AC XY: 10702 AN XY: 32914

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.359

Alfa AF: 0.211 Hom.: 9349

Bravo AF: 0.378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs933315; hg19: chrX-106598707;