rs8138122
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020070.4(IGLL1):c.566G>A(p.Arg189His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00715 in 1,613,992 control chromosomes in the GnomAD database, including 464 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.032 ( 217 hom., cov: 32)
Exomes 𝑓: 0.0045 ( 247 hom. )
Consequence
IGLL1
NM_020070.4 missense
NM_020070.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.220
Genes affected
IGLL1 (HGNC:5870): (immunoglobulin lambda like polypeptide 1) The preB cell receptor is found on the surface of proB and preB cells, where it is involved in transduction of signals for cellular proliferation, differentiation from the proB cell to the preB cell stage, allelic exclusion at the Ig heavy chain gene locus, and promotion of Ig light chain gene rearrangements. The preB cell receptor is composed of a membrane-bound Ig mu heavy chain in association with a heterodimeric surrogate light chain. This gene encodes one of the surrogate light chain subunits and is a member of the immunoglobulin gene superfamily. This gene does not undergo rearrangement. Mutations in this gene can result in B cell deficiency and agammaglobulinemia, an autosomal recessive disease in which few or no gamma globulins or antibodies are made. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0024659336).
BP6
Variant 22-23573342-C-T is Benign according to our data. Variant chr22-23573342-C-T is described in ClinVar as [Benign]. Clinvar id is 487215.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-23573342-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGLL1 | NM_020070.4 | c.566G>A | p.Arg189His | missense_variant | 3/3 | ENST00000330377.3 | |
IGLL1 | NM_001369906.1 | c.569G>A | p.Arg190His | missense_variant | 3/3 | ||
IGLL1 | NM_152855.3 | c.*195G>A | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGLL1 | ENST00000330377.3 | c.566G>A | p.Arg189His | missense_variant | 3/3 | 1 | NM_020070.4 | P1 | |
IGLL1 | ENST00000249053.3 | c.*195G>A | 3_prime_UTR_variant | 2/2 | 1 | ||||
ENST00000458318.2 | n.391-123C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
IGLL1 | ENST00000438703.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0323 AC: 4903AN: 152012Hom.: 218 Cov.: 32
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GnomAD3 exomes AF: 0.00983 AC: 2472AN: 251436Hom.: 87 AF XY: 0.00786 AC XY: 1068AN XY: 135910
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GnomAD4 exome AF: 0.00453 AC: 6617AN: 1461862Hom.: 247 Cov.: 32 AF XY: 0.00417 AC XY: 3031AN XY: 727228
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GnomAD4 genome AF: 0.0323 AC: 4917AN: 152130Hom.: 217 Cov.: 32 AF XY: 0.0320 AC XY: 2379AN XY: 74364
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Agammaglobulinemia 2, autosomal recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MPC
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at