rs12170791

Variant names:

• chr22-22199444-G-A
• rs12170791

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 0.559 in 150,792 control chromosomes in the GnomAD database, including 23,825 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 0.56 (23825 hom., cov: 28)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.559 AC: 84212 AN: 150680 Hom.: 23814 Cov.: 28

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.559 AC: 84260 AN: 150792 Hom.: 23825 Cov.: 28 AF XY: 0.560 AC XY: 41205 AN XY: 73604

African (AFR) AF: 0.625 AC: 25610 AN: 40972

American (AMR) AF: 0.569 AC: 8653 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2015 AN: 3466

East Asian (EAS) AF: 0.689 AC: 3477 AN: 5044

South Asian (SAS) AF: 0.403 AC: 1926 AN: 4780

European-Finnish (FIN) AF: 0.574 AC: 5911 AN: 10290

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 34984 AN: 67768

Other (OTH) AF: 0.538 AC: 1116 AN: 2076

Alfa AF: 0.565 Hom.: 3561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs12170791; hg19: chr22-22553845;