22-22908567-T-C

Variant names:

• chr22-22908567-T-C
• rs1475930

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 0.34 in 152,112 control chromosomes in the GnomAD database, including 10,894 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 0.34 (10894 hom., cov: 32)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• 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 (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.340 AC: 51627 AN: 151994 Hom.: 10860 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.340 AC: 51714 AN: 152112 Hom.: 10894 Cov.: 32 AF XY: 0.347 AC XY: 25820 AN XY: 74358

African (AFR) AF: 0.479 AC: 19889 AN: 41494

American (AMR) AF: 0.410 AC: 6268 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4515 AN: 5170

South Asian (SAS) AF: 0.478 AC: 2300 AN: 4814

European-Finnish (FIN) AF: 0.252 AC: 2669 AN: 10586

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13997 AN: 67974

Other (OTH) AF: 0.354 AC: 747 AN: 2112

Alfa AF: 0.257 Hom.: 26241

Bravo AF: 0.362

Asia WGS AF: 0.659 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.53
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1475930; hg19: chr22-23250737; COSMIC: COSV66545254;