rs933222

Variant names:

• chr22-37222597-T-C
• rs933222

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 0.728 in 152,058 control chromosomes in the GnomAD database, including 40,541 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 0.73 (40541 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.728 AC: 110607 AN: 151940 Hom.: 40518 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.728 AC: 110683 AN: 152058 Hom.: 40541 Cov.: 31 AF XY: 0.723 AC XY: 53720 AN XY: 74318

African (AFR) AF: 0.796 AC: 33000 AN: 41482

American (AMR) AF: 0.678 AC: 10370 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2482 AN: 3470

East Asian (EAS) AF: 0.830 AC: 4283 AN: 5158

South Asian (SAS) AF: 0.688 AC: 3313 AN: 4818

European-Finnish (FIN) AF: 0.662 AC: 6992 AN: 10562

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

European-Non Finnish (NFE) AF: 0.707 AC: 48040 AN: 67960

Other (OTH) AF: 0.718 AC: 1516 AN: 2112

Alfa AF: 0.712 Hom.: 162540

Bravo AF: 0.732

Asia WGS AF: 0.758 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.69
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs933222; hg19: chr22-37618637;