22-34545584-T-C

Variant names:

• chr22-34545584-T-C
• rs4821261

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 0.902 in 151,700 control chromosomes in the GnomAD database, including 61,818 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 0.90 (61818 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.68
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 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: 0.902 AC: 136772 AN: 151582 Hom.: 61753 Cov.: 28

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.902 AC: 136896 AN: 151700 Hom.: 61818 Cov.: 28 AF XY: 0.904 AC XY: 66975 AN XY: 74114

African (AFR) AF: 0.944 AC: 39016 AN: 41316

American (AMR) AF: 0.908 AC: 13830 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2938 AN: 3466

East Asian (EAS) AF: 0.949 AC: 4885 AN: 5148

South Asian (SAS) AF: 0.926 AC: 4450 AN: 4804

European-Finnish (FIN) AF: 0.906 AC: 9523 AN: 10514

Middle Eastern (MID) AF: 0.866 AC: 251 AN: 290

European-Non Finnish (NFE) AF: 0.873 AC: 59304 AN: 67908

Other (OTH) AF: 0.880 AC: 1852 AN: 2104

Alfa AF: 0.866 Hom.: 5245

Bravo AF: 0.904

Asia WGS AF: 0.953 AC: 3314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.018
DANN	Benign	0.080
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs4821261; hg19: chr22-34941576;