rs4824505

Variant names:

• chrX-44593652-G-A
• rs4824505

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 (2264 hom., 7260 hem., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.228 AC: 24424 AN: 107044 Hom.: 2259 Cov.: 20

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0452

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.170

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.228 AC: 24458 AN: 107076 Hom.: 2264 Cov.: 20 AF XY: 0.246 AC XY: 7260 AN XY: 29520

African (AFR) AF: 0.165 AC: 4890 AN: 29626

American (AMR) AF: 0.416 AC: 3943 AN: 9470

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 556 AN: 2607

East Asian (EAS) AF: 0.510 AC: 1708 AN: 3351

South Asian (SAS) AF: 0.443 AC: 1094 AN: 2470

European-Finnish (FIN) AF: 0.280 AC: 1437 AN: 5140

Middle Eastern (MID) AF: 0.160 AC: 34 AN: 213

European-Non Finnish (NFE) AF: 0.200 AC: 10421 AN: 52097

Other (OTH) AF: 0.240 AC: 345 AN: 1439

Alfa AF: 0.230 Hom.: 1386

Bravo AF: 0.238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.34
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4824505; hg19: chrX-44452898;