22-41361643-G-A

Variant names:

• chr22-41361643-G-A
• rs4822024

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 0.233 in 152,048 control chromosomes in the GnomAD database, including 4,992 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 0.23 (4992 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35406 AN: 151930 Hom.: 4977 Cov.: 30

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.233 AC: 35439 AN: 152048 Hom.: 4992 Cov.: 30 AF XY: 0.242 AC XY: 17964 AN XY: 74330

African (AFR) AF: 0.149 AC: 6181 AN: 41510

American (AMR) AF: 0.458 AC: 6983 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1108 AN: 3466

East Asian (EAS) AF: 0.0877 AC: 453 AN: 5164

South Asian (SAS) AF: 0.370 AC: 1783 AN: 4814

European-Finnish (FIN) AF: 0.265 AC: 2798 AN: 10550

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15138 AN: 67972

Other (OTH) AF: 0.274 AC: 578 AN: 2112

Alfa AF: 0.221 Hom.: 11730

Bravo AF: 0.247

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4822024; hg19: chr22-41757647;