rs5750720

Variant names:

• chr22-22208677-C-A
• rs5750720

Your query was ambiguous. Multiple possible variants found:

• chr22-22208677-C-A
• chr22-22208677-C-T

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 0.327 in 151,066 control chromosomes in the GnomAD database, including 8,744 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 0.33 (8744 hom., cov: 32)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGL		n.22208677C>A		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49463 AN: 150950 Hom.: 8748 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.327 AC: 49466 AN: 151066 Hom.: 8744 Cov.: 32 AF XY: 0.332 AC XY: 24515 AN XY: 73842

African (AFR) AF: 0.199 AC: 8116 AN: 40770

American (AMR) AF: 0.381 AC: 5807 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3466

East Asian (EAS) AF: 0.492 AC: 2528 AN: 5142

South Asian (SAS) AF: 0.372 AC: 1790 AN: 4810

European-Finnish (FIN) AF: 0.419 AC: 4388 AN: 10474

Middle Eastern (MID) AF: 0.240 AC: 69 AN: 288

European-Non Finnish (NFE) AF: 0.363 AC: 24656 AN: 67874

Other (OTH) AF: 0.307 AC: 645 AN: 2100

Alfa AF: 0.275 Hom.: 1145

Bravo AF: 0.319

Asia WGS AF: 0.423 AC: 1468 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.30
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs5750720; hg19: chr22-22563068;