rs2858719

Variant names:

• chrX-86905129-C-A
• rs2858719

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 0.286 in 109,803 control chromosomes in the GnomAD database, including 4,427 homozygotes. There are 8,912 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 (4427 hom., 8912 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 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: 0.286 AC: 31381 AN: 109763 Hom.: 4424 Cov.: 22 AF XY: 0.277 AC XY: 8893 AN XY: 32135

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.0617

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.286 AC: 31407 AN: 109803 Hom.: 4427 Cov.: 22 AF XY: 0.277 AC XY: 8912 AN XY: 32185

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.280

Alfa AF: 0.194 Hom.: 4275

Bravo AF: 0.325

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858719; hg19: chrX-86160132;