chrX-12892500-T-G

Position:

• chrX-12892500-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 0.432 in 110,839 control chromosomes in the GnomAD database, including 7,652 homozygotes. There are 13,586 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 (7652 hom., 13586 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 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: 0.432 AC: 47840 AN: 110785 Hom.: 7652 Cov.: 23 AF XY: 0.411 AC XY: 13561 AN XY: 33029

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.432 AC: 47864 AN: 110839 Hom.: 7652 Cov.: 23 AF XY: 0.411 AC XY: 13586 AN XY: 33093

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.417

Alfa AF: 0.438 Hom.: 17308

Bravo AF: 0.428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.99
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2269809; hg19: chrX-12910619;