rs10482283

Variant names:

• chrX-24451605-G-A
• rs10482283

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 0.293 in 109,065 control chromosomes in the GnomAD database, including 5,528 homozygotes. There are 8,572 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 0.29 (5528 hom., 8572 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

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 (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.293 AC: 31896 AN: 109015 Hom.: 5524 Cov.: 21 AF XY: 0.272 AC XY: 8533 AN XY: 31395

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0897

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.293 AC: 31944 AN: 109065 Hom.: 5528 Cov.: 21 AF XY: 0.273 AC XY: 8572 AN XY: 31455

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.0894

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.278

Alfa AF: 0.193 Hom.: 5858

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.068
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10482283; hg19: chrX-24469722;