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. The variant received -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
• Publications: 4 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 = 0.204 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: 0.112 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

African (AFR) AF: 0.0818 AC: 3395 AN: 41494

American (AMR) AF: 0.158 AC: 2416 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3470

East Asian (EAS) AF: 0.0638 AC: 330 AN: 5170

South Asian (SAS) AF: 0.215 AC: 1034 AN: 4818

European-Finnish (FIN) AF: 0.0665 AC: 705 AN: 10596

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8089 AN: 67978

Other (OTH) AF: 0.123 AC: 260 AN: 2106

Alfa AF: 0.123 Hom.: 1763

Bravo AF: 0.115

Asia WGS AF: 0.139 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.93
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4824093; hg19: chr22-50128268;