22-22616398-T-C

Variant names:

• chr22-22616398-T-C
• rs5759068

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 0.654 in 151,608 control chromosomes in the GnomAD database, including 32,821 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 (32821 hom., cov: 31)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 4 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.654 AC: 99111 AN: 151488 Hom.: 32763 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.654 AC: 99227 AN: 151608 Hom.: 32821 Cov.: 31 AF XY: 0.660 AC XY: 48868 AN XY: 74062

African (AFR) AF: 0.673 AC: 27830 AN: 41368

American (AMR) AF: 0.709 AC: 10790 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2091 AN: 3462

East Asian (EAS) AF: 0.863 AC: 4327 AN: 5012

South Asian (SAS) AF: 0.798 AC: 3829 AN: 4796

European-Finnish (FIN) AF: 0.638 AC: 6742 AN: 10560

Middle Eastern (MID) AF: 0.674 AC: 190 AN: 282

European-Non Finnish (NFE) AF: 0.610 AC: 41440 AN: 67906

Other (OTH) AF: 0.683 AC: 1435 AN: 2100

Alfa AF: 0.638 Hom.: 10989

Asia WGS AF: 0.791 AC: 2749 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.22
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs5759068; hg19: chr22-22958868;