rs74519217
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_020070.4(IGLL1):c.507C>T(p.Ser169=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00367 in 1,614,034 control chromosomes in the GnomAD database, including 159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.019 ( 73 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 86 hom. )
Consequence
IGLL1
NM_020070.4 synonymous
NM_020070.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00300
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 22-23573401-G-A is Benign according to our data. Variant chr22-23573401-G-A is described in ClinVar as [Benign]. Clinvar id is 471478.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.003 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0631 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGLL1 | NM_020070.4 | c.507C>T | p.Ser169= | synonymous_variant | 3/3 | ENST00000330377.3 | |
IGLL1 | NM_001369906.1 | c.510C>T | p.Ser170= | synonymous_variant | 3/3 | ||
IGLL1 | NM_152855.3 | c.*136C>T | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGLL1 | ENST00000330377.3 | c.507C>T | p.Ser169= | synonymous_variant | 3/3 | 1 | NM_020070.4 | P1 | |
IGLL1 | ENST00000249053.3 | c.*136C>T | 3_prime_UTR_variant | 2/2 | 1 | ||||
ENST00000458318.2 | n.391-64G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
IGLL1 | ENST00000438703.1 | c.510C>T | p.Ser170= | synonymous_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0188 AC: 2863AN: 152130Hom.: 73 Cov.: 32
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GnomAD3 exomes AF: 0.00509 AC: 1279AN: 251448Hom.: 33 AF XY: 0.00364 AC XY: 494AN XY: 135890
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GnomAD4 exome AF: 0.00210 AC: 3064AN: 1461786Hom.: 86 Cov.: 32 AF XY: 0.00180 AC XY: 1307AN XY: 727190
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GnomAD4 genome ? AF: 0.0188 AC: 2867AN: 152248Hom.: 73 Cov.: 32 AF XY: 0.0181 AC XY: 1345AN XY: 74430
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Agammaglobulinemia 2, autosomal recessive Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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