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.

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: 0.377 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 v4.9

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;