rs4820293

Variant names:

• chr22-37674914-A-G
• rs4820293

Your query was ambiguous. Multiple possible variants found:

• chr22-37674914-A-G
• chr22-37674914-A-T

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 0.653 in 152,098 control chromosomes in the GnomAD database, including 33,200 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 0.65 (33200 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99172 AN: 151980 Hom.: 33162 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.653 AC: 99262 AN: 152098 Hom.: 33200 Cov.: 33 AF XY: 0.652 AC XY: 48458 AN XY: 74356

African (AFR) AF: 0.796 AC: 33070 AN: 41520

American (AMR) AF: 0.697 AC: 10658 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2326 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3110 AN: 5174

South Asian (SAS) AF: 0.596 AC: 2861 AN: 4804

European-Finnish (FIN) AF: 0.538 AC: 5688 AN: 10574

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.578 AC: 39301 AN: 67946

Other (OTH) AF: 0.668 AC: 1413 AN: 2114

Alfa AF: 0.616 Hom.: 12645

Bravo AF: 0.673

Asia WGS AF: 0.644 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.38
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4820293; hg19: chr22-38070921;