22-32188672-A-G

Position:

• chr22-32188672-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 0.538 in 152,112 control chromosomes in the GnomAD database, including 24,228 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 0.54 (24228 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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: 0.538 AC: 81770 AN: 151994 Hom.: 24180 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.538 AC: 81875 AN: 152112 Hom.: 24228 Cov.: 33 AF XY: 0.528 AC XY: 39235 AN XY: 74336

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.506

Alfa AF: 0.401 Hom.: 1638

Bravo AF: 0.550

Asia WGS AF: 0.352 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs136457; hg19: chr22-32584659;