22-26814728-A-G

Position:

• chr22-26814728-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.728 in 152,136 control chromosomes in the GnomAD database, including 40,658 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 0.73 (40658 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.80

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110704 AN: 152018 Hom.: 40625 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.728 AC: 110785 AN: 152136 Hom.: 40658 Cov.: 33 AF XY: 0.722 AC XY: 53688 AN XY: 74354

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.754

Alfa AF: 0.767 Hom.: 60088

Bravo AF: 0.725

Asia WGS AF: 0.619 AC: 2150 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	22
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713974; hg19: chr22-27210691;