chr15-22832212-A-G

Variant names:

• chr15-22832212-A-G
• rs4778334

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 0.722 in 151,822 control chromosomes in the GnomAD database, including 40,322 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 0.72 (40322 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109496 AN: 151704 Hom.: 40306 Cov.: 30

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.722 AC: 109557 AN: 151822 Hom.: 40322 Cov.: 30 AF XY: 0.729 AC XY: 54061 AN XY: 74184

African (AFR) AF: 0.577 AC: 23845 AN: 41318

American (AMR) AF: 0.766 AC: 11681 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2535 AN: 3472

East Asian (EAS) AF: 0.900 AC: 4636 AN: 5150

South Asian (SAS) AF: 0.729 AC: 3513 AN: 4822

European-Finnish (FIN) AF: 0.863 AC: 9106 AN: 10554

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51787 AN: 67946

Other (OTH) AF: 0.705 AC: 1485 AN: 2106

Alfa AF: 0.746 Hom.: 149897

Bravo AF: 0.712

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.49
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs4778334; hg19: chr15-23040856;