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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGL		n.22908567T>C		intragenic_variant

Ensembl

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

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 v4.3

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;