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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0785 AC: 3073 AN: 39150

American (AMR) AF: 0.272 AC: 3857 AN: 14206

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 768 AN: 3424

East Asian (EAS) AF: 0.405 AC: 1939 AN: 4792

South Asian (SAS) AF: 0.418 AC: 1903 AN: 4558

European-Finnish (FIN) AF: 0.361 AC: 2893 AN: 8022

Middle Eastern (MID) AF: 0.207 AC: 56 AN: 270

European-Non Finnish (NFE) AF: 0.273 AC: 18131 AN: 66296

Other (OTH) AF: 0.261 AC: 518 AN: 1988

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs34808254; hg19: chrX-820518;