rs2330040

Variant names:

• chr22-22213371-G-A
• rs2330040

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 0.593 in 151,358 control chromosomes in the GnomAD database, including 27,597 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 0.59 (27597 hom., cov: 29)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.705 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: 0.593 AC: 89751 AN: 151234 Hom.: 27574 Cov.: 29

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.593 AC: 89820 AN: 151358 Hom.: 27597 Cov.: 29 AF XY: 0.600 AC XY: 44353 AN XY: 73906

African (AFR) AF: 0.461 AC: 19007 AN: 41192

American (AMR) AF: 0.552 AC: 8387 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1938 AN: 3472

East Asian (EAS) AF: 0.663 AC: 3378 AN: 5096

South Asian (SAS) AF: 0.725 AC: 3454 AN: 4764

European-Finnish (FIN) AF: 0.790 AC: 8283 AN: 10490

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43408 AN: 67864

Other (OTH) AF: 0.565 AC: 1183 AN: 2094

Alfa AF: 0.617 Hom.: 12758

Asia WGS AF: 0.725 AC: 2520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.61
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2330040; hg19: chr22-22567762;