22-22180754-A-G

Variant names:

• chr22-22180754-A-G
• rs713624

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 0.349 in 151,816 control chromosomes in the GnomAD database, including 9,614 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 0.35 (9614 hom., cov: 33)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 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: 0.349 AC: 52930 AN: 151704 Hom.: 9597 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.349 AC: 52994 AN: 151816 Hom.: 9614 Cov.: 33 AF XY: 0.357 AC XY: 26520 AN XY: 74204

African (AFR) AF: 0.319 AC: 13217 AN: 41406

American (AMR) AF: 0.437 AC: 6663 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 964 AN: 3460

East Asian (EAS) AF: 0.658 AC: 3374 AN: 5128

South Asian (SAS) AF: 0.488 AC: 2348 AN: 4808

European-Finnish (FIN) AF: 0.356 AC: 3748 AN: 10534

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21572 AN: 67920

Other (OTH) AF: 0.344 AC: 725 AN: 2108

Alfa AF: 0.351 Hom.: 3392

Bravo AF: 0.356

Asia WGS AF: 0.564 AC: 1958 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs713624;

hg19: chr22-22535144;