rs4824505

chrX-44593652-G-A

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 0.228 in 107,076 control chromosomes in the GnomAD database, including 2,264 homozygotes. There are 7,260 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 (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/exons	MANE	UniProt

Ensembl

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