rs134797

Variant names:

• chr22-27273875-C-T
• rs134797

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;