rs4824093

Variant names:

• chr22-49734620-G-A
• rs4824093

Your query was ambiguous. Multiple possible variants found:

• chr22-49734620-G-A
• chr22-49734620-G-C

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 0.112 in 152,106 control chromosomes in the GnomAD database, including 1,002 homozygotes. 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 0.11 (1002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

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 = 0.204 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: 0.112 AC: 16996 AN: 151988 Hom.: 1002 Cov.: 32

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0637

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.112 AC: 17007 AN: 152106 Hom.: 1002 Cov.: 32 AF XY: 0.111 AC XY: 8243 AN XY: 74348

Gnomad4 AFR AF: 0.0818

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0638

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.123

Alfa AF: 0.125 Hom.: 1218

Bravo AF: 0.115

Asia WGS AF: 0.139 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4824093; hg19: chr22-50128268;