chr22-28765019-C-T

Position:

• chr22-28765019-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 0.215 in 151,772 control chromosomes in the GnomAD database, including 3,809 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 0.22 (3809 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.28765019C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32600 AN: 151654 Hom.: 3807 Cov.: 30

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.215 AC: 32645 AN: 151772 Hom.: 3809 Cov.: 30 AF XY: 0.218 AC XY: 16139 AN XY: 74162

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.235

Alfa AF: 0.178 Hom.: 305

Bravo AF: 0.229

Asia WGS AF: 0.338 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
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: rs4820792; hg19: chr22-29161007;