X-12828116-A-T

Position:

• chrX-12828116-A-T

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 0.309 in 110,826 control chromosomes in the GnomAD database, including 4,198 homozygotes. There are 10,257 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 0.31 (4198 hom., 10257 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.310 AC: 34299 AN: 110770 Hom.: 4204 Cov.: 22 AF XY: 0.310 AC XY: 10243 AN XY: 33018

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.309 AC: 34298 AN: 110826 Hom.: 4198 Cov.: 22 AF XY: 0.310 AC XY: 10257 AN XY: 33084

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.317

Alfa AF: 0.334 Hom.: 2195

Bravo AF: 0.305

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6641116; hg19: chrX-12846235;