X-12902467-A-G

Position:

• chrX-12902467-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 0.188 in 110,894 control chromosomes in the GnomAD database, including 1,643 homozygotes. There are 5,901 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 0.19 (1643 hom., 5901 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 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: 0.188 AC: 20798 AN: 110840 Hom.: 1644 Cov.: 22 AF XY: 0.178 AC XY: 5891 AN XY: 33120

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.00643

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.188 AC: 20808 AN: 110894 Hom.: 1643 Cov.: 22 AF XY: 0.178 AC XY: 5901 AN XY: 33184

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.00645

Gnomad4 SAS AF: 0.0891

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.163

Alfa AF: 0.194 Hom.: 1109

Bravo AF: 0.191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs178995; hg19: chrX-12920586;