rs134797

chr22-27273875-C-T

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 0.396 in 150,770 control chromosomes in the GnomAD database, including 12,705 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 0.40 (12705 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -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 = 0.591 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: 0.396 AC: 59663 AN: 150668 Hom.: 12691 Cov.: 28

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.396 AC: 59695 AN: 150770 Hom.: 12705 Cov.: 28 AF XY: 0.405 AC XY: 29773 AN XY: 73550

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.385

Alfa AF: 0.406 Hom.: 2682

Bravo AF: 0.386

Asia WGS AF: 0.583 AC: 2026 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.73
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs134797; hg19: chr22-27669836;