rs987710

Variant names:

• chr22-22158022-G-A
• rs987710

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 0.612 in 151,904 control chromosomes in the GnomAD database, including 29,439 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 0.61 (29439 hom., cov: 31)
• Consequence: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 10 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 (AMR) allele frequency at 95% confidence interval = 0.67 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: 0.612 AC: 92967 AN: 151790 Hom.: 29443 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.612 AC: 92978 AN: 151904 Hom.: 29439 Cov.: 31 AF XY: 0.619 AC XY: 45972 AN XY: 74264

African (AFR) AF: 0.440 AC: 18241 AN: 41418

American (AMR) AF: 0.681 AC: 10394 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2245 AN: 3466

East Asian (EAS) AF: 0.675 AC: 3478 AN: 5150

South Asian (SAS) AF: 0.624 AC: 2998 AN: 4806

European-Finnish (FIN) AF: 0.757 AC: 7972 AN: 10532

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45595 AN: 67954

Other (OTH) AF: 0.618 AC: 1306 AN: 2114

Alfa AF: 0.627 Hom.: 37337

Bravo AF: 0.600

Asia WGS AF: 0.604 AC: 2096 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.58
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs987710; hg19: chr22-22512415;