rs228921

Variant names:

• chr22-37110836-A-G
• rs228921

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.406 in 151,914 control chromosomes in the GnomAD database, including 12,640 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 0.41 (12640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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: 0.406 AC: 61565 AN: 151796 Hom.: 12611 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.406 AC: 61644 AN: 151914 Hom.: 12640 Cov.: 32 AF XY: 0.407 AC XY: 30227 AN XY: 74258

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.402

Alfa AF: 0.417 Hom.: 21480

Bravo AF: 0.393

Asia WGS AF: 0.485 AC: 1690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228921; hg19: chr22-37506876;