rs6000790

Variant names:

• chr22-22061882-A-G
• rs6000790

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 0.203 in 152,000 control chromosomes in the GnomAD database, including 3,288 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 0.20 (3288 hom., cov: 32)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 3 publications found

Genes affected

IGL (HGNC:5853):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 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: 0.203 AC: 30819 AN: 151882 Hom.: 3283 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0358

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.203 AC: 30852 AN: 152000 Hom.: 3288 Cov.: 32 AF XY: 0.201 AC XY: 14899 AN XY: 74278

African (AFR) AF: 0.171 AC: 7094 AN: 41468

American (AMR) AF: 0.196 AC: 2993 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3470

East Asian (EAS) AF: 0.0361 AC: 186 AN: 5158

South Asian (SAS) AF: 0.180 AC: 868 AN: 4810

European-Finnish (FIN) AF: 0.227 AC: 2399 AN: 10564

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15887 AN: 67932

Other (OTH) AF: 0.209 AC: 442 AN: 2112

Alfa AF: 0.211 Hom.: 371

Bravo AF: 0.196

Asia WGS AF: 0.157 AC: 547 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6000790; hg19: chr22-22416297;