rs4824505

Variant names:

• chrX-44593652-G-A
• rs4824505

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.228 AC: 24424 AN: 107044 Hom.: 2259 Cov.: 20 AF XY: 0.245 AC XY: 7234 AN XY: 29478

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

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.240

Alfa AF: 0.230 Hom.: 1386

Bravo AF: 0.238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4824505; hg19: chrX-44452898;