22-45432666-G-A

Position:

• chr22-45432666-G-A

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 0.275 in 152,112 control chromosomes in the GnomAD database, including 6,601 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 0.27 (6601 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 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: 0.275 AC: 41725 AN: 151994 Hom.: 6582 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.275 AC: 41796 AN: 152112 Hom.: 6601 Cov.: 33 AF XY: 0.275 AC XY: 20464 AN XY: 74362

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.260

Alfa AF: 0.218 Hom.: 6071

Bravo AF: 0.279

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11913200; hg19: chr22-45828546;