rs133980

Positions:

• chr22-27626764-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 0.422 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.447

Alfa AF: 0.466 Hom.: 10197

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs133980; hg19: chr22-28022728;