X-920268-A-G

Position:

• chrX-920268-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 0.506 in 151,802 control chromosomes in the GnomAD database, including 20,093 homozygotes. There are 37,776 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 0.51 (20093 hom., 37776 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76786 AN: 151684 Hom.: 20063 Cov.: 31 AF XY: 0.509 AC XY: 37687 AN XY: 74036

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.506 AC: 76864 AN: 151802 Hom.: 20093 Cov.: 31 AF XY: 0.509 AC XY: 37776 AN XY: 74164

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.499

Bravo AF: 0.513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	3.7
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988300; hg19: chrX-881003;