rs4820556

Variant names:

• chr22-23530749-A-G
• rs4820556

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 0.311 in 151,834 control chromosomes in the GnomAD database, including 7,942 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 0.31 (7942 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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: 0.311 AC: 47171 AN: 151716 Hom.: 7938 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.311 AC: 47214 AN: 151834 Hom.: 7942 Cov.: 31 AF XY: 0.305 AC XY: 22642 AN XY: 74160

African (AFR) AF: 0.444 AC: 18382 AN: 41376

American (AMR) AF: 0.279 AC: 4255 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1132 AN: 3462

East Asian (EAS) AF: 0.197 AC: 1010 AN: 5122

South Asian (SAS) AF: 0.181 AC: 870 AN: 4810

European-Finnish (FIN) AF: 0.206 AC: 2176 AN: 10580

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18442 AN: 67904

Other (OTH) AF: 0.306 AC: 646 AN: 2108

Alfa AF: 0.283 Hom.: 3956

Bravo AF: 0.326

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.33
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs4820556; hg19: chr22-23872936;