rs133980

Variant names:

• chr22-27626764-A-G
• rs133980

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 0.422 in 152,024 control chromosomes in the GnomAD database, including 14,286 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 0.42 (14286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.49 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: 0.422 AC: 64134 AN: 151906 Hom.: 14284 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.422 AC: 64140 AN: 152024 Hom.: 14286 Cov.: 32 AF XY: 0.424 AC XY: 31467 AN XY: 74286

African (AFR) AF: 0.275 AC: 11390 AN: 41458

American (AMR) AF: 0.432 AC: 6604 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1835 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1575 AN: 5164

South Asian (SAS) AF: 0.502 AC: 2420 AN: 4818

European-Finnish (FIN) AF: 0.490 AC: 5170 AN: 10550

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33612 AN: 67966

Other (OTH) AF: 0.447 AC: 946 AN: 2116

Alfa AF: 0.469 Hom.: 41194

Bravo AF: 0.407

Asia WGS AF: 0.382 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs133980; hg19: chr22-28022728;