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.

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: 0.328 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 v4.9

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;