X-146304706-T-C

Position:

• chrX-146304706-T-C

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 0.427 in 110,918 control chromosomes in the GnomAD database, including 7,373 homozygotes. There are 14,189 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 0.43 (7373 hom., 14189 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 47357 AN: 110858 Hom.: 7368 Cov.: 23 AF XY: 0.427 AC XY: 14148 AN XY: 33110

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.427 AC: 47405 AN: 110918 Hom.: 7373 Cov.: 23 AF XY: 0.428 AC XY: 14189 AN XY: 33180

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.445

Alfa AF: 0.445 Hom.: 22497

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1339482; hg19: chrX-145386224;