rs133545

chr22-48235872-C-A

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 0.108 in 152,230 control chromosomes in the GnomAD database, including 1,081 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 0.11 (1081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

ACMG classification

Verdict is Benign. Variant got -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 = 0.181 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: 0.108 AC: 16373 AN: 152112 Hom.: 1080 Cov.: 32

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.108 AC: 16387 AN: 152230 Hom.: 1081 Cov.: 32 AF XY: 0.109 AC XY: 8075 AN XY: 74412

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.111

Alfa AF: 0.127 Hom.: 1751

Bravo AF: 0.0990

Asia WGS AF: 0.184 AC: 642 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	2.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs133545; hg19: chr22-48631684;