22-41667677-A-G

Variant names:

• chr22-41667677-A-G
• rs132793

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.834 in 152,052 control chromosomes in the GnomAD database, including 53,858 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 0.83 (53858 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.39
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126687 AN: 151934 Hom.: 53797 Cov.: 30

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.834 AC: 126802 AN: 152052 Hom.: 53858 Cov.: 30 AF XY: 0.825 AC XY: 61315 AN XY: 74310

African (AFR) AF: 0.957 AC: 39742 AN: 41512

American (AMR) AF: 0.642 AC: 9799 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4867 AN: 5162

South Asian (SAS) AF: 0.704 AC: 3386 AN: 4812

European-Finnish (FIN) AF: 0.776 AC: 8192 AN: 10554

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55734 AN: 67974

Other (OTH) AF: 0.806 AC: 1700 AN: 2110

Alfa AF: 0.805 Hom.: 60164

Bravo AF: 0.826

Asia WGS AF: 0.846 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.33
PhyloP100		-4.4

Splicing

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

Other links and lift over

dbSNP: rs132793; hg19: chr22-42063681;