22-28849243-T-G

Variant names:

• chr22-28849243-T-G
• rs5762853

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 0.309 in 151,740 control chromosomes in the GnomAD database, including 8,117 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 0.31 (8117 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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: 0.309 AC: 46813 AN: 151622 Hom.: 8104 Cov.: 29

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.309 AC: 46875 AN: 151740 Hom.: 8117 Cov.: 29 AF XY: 0.313 AC XY: 23202 AN XY: 74144

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.318

Alfa AF: 0.268 Hom.: 958

Bravo AF: 0.309

Asia WGS AF: 0.579 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5762853; hg19: chr22-29245231;