chr22-32188723-G-C

Position:

• chr22-32188723-G-C

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 0.539 in 152,022 control chromosomes in the GnomAD database, including 24,227 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 (24227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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 = 0.773 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: 81760 AN: 151906 Hom.: 24179 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.385

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: 0.539 AC: 81865 AN: 152022 Hom.: 24227 Cov.: 32 AF XY: 0.528 AC XY: 39253 AN XY: 74300

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.506

Alfa AF: 0.343 Hom.: 806

Bravo AF: 0.550

Asia WGS AF: 0.352 AC: 1223 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	0.76
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: rs136458; hg19: chr22-32584710;