22-22158022-G-A

Variant names:

• chr22-22158022-G-A
• rs987710

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 0.612 in 151,904 control chromosomes in the GnomAD database, including 29,439 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 0.61 (29439 hom., cov: 31)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 10 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGL		n.22158022G>A		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92967 AN: 151790 Hom.: 29443 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.612 AC: 92978 AN: 151904 Hom.: 29439 Cov.: 31 AF XY: 0.619 AC XY: 45972 AN XY: 74264

African (AFR) AF: 0.440 AC: 18241 AN: 41418

American (AMR) AF: 0.681 AC: 10394 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2245 AN: 3466

East Asian (EAS) AF: 0.675 AC: 3478 AN: 5150

South Asian (SAS) AF: 0.624 AC: 2998 AN: 4806

European-Finnish (FIN) AF: 0.757 AC: 7972 AN: 10532

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45595 AN: 67954

Other (OTH) AF: 0.618 AC: 1306 AN: 2114

Alfa AF: 0.627 Hom.: 37337

Bravo AF: 0.600

Asia WGS AF: 0.604 AC: 2096 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.58
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs987710; hg19: chr22-22512415;