22-19588430-A-G

Variant names:

• chr22-19588430-A-G
• rs737857

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 0.0834 in 152,234 control chromosomes in the GnomAD database, including 706 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 0.083 (706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12699 AN: 152116 Hom.: 706 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.0834 AC: 12702 AN: 152234 Hom.: 706 Cov.: 32 AF XY: 0.0857 AC XY: 6376 AN XY: 74408

African (AFR) AF: 0.0230 AC: 955 AN: 41556

American (AMR) AF: 0.0693 AC: 1059 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 508 AN: 3470

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5188

South Asian (SAS) AF: 0.122 AC: 586 AN: 4812

European-Finnish (FIN) AF: 0.141 AC: 1492 AN: 10582

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7647 AN: 68022

Other (OTH) AF: 0.0870 AC: 184 AN: 2116

Alfa AF: 0.0923 Hom.: 133

Bravo AF: 0.0739

Asia WGS AF: 0.0640 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.63
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs737857; hg19: chr22-19575953;