22-28794483-T-C

Position:

• chr22-28794483-T-C

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 0.115 in 152,420 control chromosomes in the GnomAD database, including 1,183 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 0.11 (1181 hom., cov: 32)
  • Exomes 𝑓: 0.17 (2 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.268 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: 0.115 AC: 17487 AN: 152158 Hom.: 1183 Cov.: 32

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.167 AC: 24 AN: 144 Hom.: 2 AF XY: 0.176 AC XY: 13 AN XY: 74

Gnomad4 EAS exome AF: 0.172

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.115 AC: 17480 AN: 152276 Hom.: 1181 Cov.: 32 AF XY: 0.116 AC XY: 8603 AN XY: 74464

Gnomad4 AFR AF: 0.0658

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.138

Alfa AF: 0.119 Hom.: 467

Bravo AF: 0.110

Asia WGS AF: 0.239 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2267131; hg19: chr22-29190471;