rs34808254

Variant names:

• chrX-859783-G-A
• rs34808254

Your query was ambiguous. Multiple possible variants found:

• chrX-859783-G-A
• chrX-859783-G-C
• chrX-859783-G-T

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 0.232 in 143,604 control chromosomes in the GnomAD database, including 4,772 homozygotes. There are 16,692 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 0.23 (4772 hom., 16692 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 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: 0.232 AC: 33346 AN: 143550 Hom.: 4764 Cov.: 24 AF XY: 0.241 AC XY: 16684 AN XY: 69230

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.232 AC: 33359 AN: 143604 Hom.: 4772 Cov.: 24 AF XY: 0.241 AC XY: 16692 AN XY: 69298

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.261

Bravo AF: 0.217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34808254; hg19: chrX-820518;