rs4819833

Variant names:

• chr22-19703979-T-C
• rs4819833

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 0.699 in 152,164 control chromosomes in the GnomAD database, including 37,800 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 0.70 (37800 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 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: 0.699 AC: 106235 AN: 152046 Hom.: 37748 Cov.: 33

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.699 AC: 106343 AN: 152164 Hom.: 37800 Cov.: 33 AF XY: 0.691 AC XY: 51413 AN XY: 74378

African (AFR) AF: 0.831 AC: 34540 AN: 41546

American (AMR) AF: 0.737 AC: 11274 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2312 AN: 3472

East Asian (EAS) AF: 0.488 AC: 2518 AN: 5164

South Asian (SAS) AF: 0.690 AC: 3325 AN: 4822

European-Finnish (FIN) AF: 0.541 AC: 5719 AN: 10566

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44428 AN: 67988

Other (OTH) AF: 0.679 AC: 1436 AN: 2116

Alfa AF: 0.669 Hom.: 62755

Bravo AF: 0.717

Asia WGS AF: 0.639 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs4819833; hg19: chr22-19691502;