rs2877021

Variant names:

• chr22-22165909-G-A
• rs2877021

Your query was ambiguous. Multiple possible variants found:

• chr22-22165909-G-A
• chr22-22165909-G-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 0.377 in 152,000 control chromosomes in the GnomAD database, including 11,632 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 0.38 (11632 hom., cov: 32)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGL		n.22165909G>A		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57229 AN: 151880 Hom.: 11611 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.377 AC: 57292 AN: 152000 Hom.: 11632 Cov.: 32 AF XY: 0.383 AC XY: 28420 AN XY: 74292

African (AFR) AF: 0.507 AC: 21018 AN: 41458

American (AMR) AF: 0.409 AC: 6258 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2703 AN: 5124

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4814

European-Finnish (FIN) AF: 0.369 AC: 3906 AN: 10574

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19548 AN: 67962

Other (OTH) AF: 0.335 AC: 706 AN: 2110

Alfa AF: 0.288 Hom.: 3267

Bravo AF: 0.387

Asia WGS AF: 0.421 AC: 1459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.84
DANN	Benign	0.46
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2877021; hg19: chr22-22520302;