22-37222038-A-G

Variant names:

• chr22-37222038-A-G
• rs4821609

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 0.721 in 152,128 control chromosomes in the GnomAD database, including 39,771 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 (39771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.721 AC: 109673 AN: 152008 Hom.: 39751 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.721 AC: 109745 AN: 152128 Hom.: 39771 Cov.: 32 AF XY: 0.717 AC XY: 53292 AN XY: 74366

African (AFR) AF: 0.773 AC: 32072 AN: 41494

American (AMR) AF: 0.676 AC: 10328 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2478 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4313 AN: 5182

South Asian (SAS) AF: 0.688 AC: 3317 AN: 4820

European-Finnish (FIN) AF: 0.662 AC: 7008 AN: 10582

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48036 AN: 67976

Other (OTH) AF: 0.712 AC: 1504 AN: 2112

Alfa AF: 0.715 Hom.: 5880

Bravo AF: 0.724

Asia WGS AF: 0.754 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.49
DANN	Benign	0.34
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4821609; hg19: chr22-37618078;