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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGL		n.22616398T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;