rs228921

chr22-37110836-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;