22-32179227-A-G

Position:

• chr22-32179227-A-G

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 0.337 in 152,120 control chromosomes in the GnomAD database, including 9,677 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 0.34 (9677 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32179227A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51227 AN: 152002 Hom.: 9652 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.337 AC: 51299 AN: 152120 Hom.: 9677 Cov.: 32 AF XY: 0.333 AC XY: 24797 AN XY: 74376

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.0906

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.295

Alfa AF: 0.324 Hom.: 1451

Bravo AF: 0.338

Asia WGS AF: 0.245 AC: 851 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	3.7
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs136416; hg19: chr22-32575214;