rs34808254

chrX-859783-G-AchrX-859783-G-CchrX-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;