rs133845

Variant names:

• chr22-25736872-A-C
• rs133845

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 0.544 in 151,732 control chromosomes in the GnomAD database, including 24,396 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 0.54 (24396 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.544 AC: 82436 AN: 151614 Hom.: 24336 Cov.: 29

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.544 AC: 82565 AN: 151732 Hom.: 24396 Cov.: 29 AF XY: 0.550 AC XY: 40777 AN XY: 74142

African (AFR) AF: 0.762 AC: 31549 AN: 41388

American (AMR) AF: 0.564 AC: 8603 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1285 AN: 3464

East Asian (EAS) AF: 0.792 AC: 4070 AN: 5142

South Asian (SAS) AF: 0.626 AC: 2994 AN: 4786

European-Finnish (FIN) AF: 0.443 AC: 4659 AN: 10510

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27838 AN: 67874

Other (OTH) AF: 0.516 AC: 1086 AN: 2106

Alfa AF: 0.478 Hom.: 39338

Bravo AF: 0.562

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.60
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs133845; hg19: chr22-26132839;