dbSNP rs16993280: IGL:n.22814988G>A (chr22-22814988-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.146 in 151,166 control chromosomes in the GnomAD database, including 1,871 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 0.15 ( 1870 hom., cov: 31)

Exomes 𝑓: 0.11 ( 1 hom. )

Consequence

IGL
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.273

Variant links:

Genes affected

IGL (HGNC:5853):

IGL links:

ENSG00000289120 (HGNC:):

ENSG00000289120 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGL		n.22814988G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000289120	ENST00000686504.1 link	n.208+3395C>T	intron_variant	Intron 2 of 3
ENSG00000289120	ENST00000702002.1 link	n.207+3395C>T	intron_variant	Intron 2 of 2
ENSG00000226477	ENST00000423259.1 link	n.*62G>A	downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22001

AN:

150882

Hom.:

1871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.0956

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.000406

Gnomad SAS

AF:

0.0447

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.111

AC:

AN:

180

Hom.:

AF XY:

0.0956

AC XY:

AN XY:

136

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.357

Gnomad4 NFE exome

AF:

0.106

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.146

AC:

22006

AN:

150986

Hom.:

1870

Cov.:

AF XY:

0.142

AC XY:

10462

AN XY:

73704

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.0955

Gnomad4 ASJ

AF:

0.126

Gnomad4 EAS

AF:

0.000611

Gnomad4 SAS

AF:

0.0452

Gnomad4 FIN

AF:

0.145

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.129

Alfa

AF:

0.138

Hom.:

221

Bravo

AF:

0.147

Asia WGS

AF:

0.0350

AC:

123

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.39

DANN

Benign

0.67

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over