rs6009824

Variant names:

• chr22-49692725-G-A
• rs6009824

Your query was ambiguous. Multiple possible variants found:

• chr22-49692725-G-A
• chr22-49692725-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 0.229 in 152,150 control chromosomes in the GnomAD database, including 4,829 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 0.23 (4829 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.903
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.229 AC: 34835 AN: 152030 Hom.: 4813 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.229 AC: 34900 AN: 152150 Hom.: 4829 Cov.: 33 AF XY: 0.229 AC XY: 17071 AN XY: 74386

African (AFR) AF: 0.378 AC: 15677 AN: 41472

American (AMR) AF: 0.149 AC: 2278 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3472

East Asian (EAS) AF: 0.150 AC: 775 AN: 5170

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4822

European-Finnish (FIN) AF: 0.167 AC: 1769 AN: 10602

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11263 AN: 67994

Other (OTH) AF: 0.223 AC: 472 AN: 2112

Alfa AF: 0.190 Hom.: 5963

Bravo AF: 0.232

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.60
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs6009824; hg19: chr22-50086373;