22-23573284-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020070.4(IGLL1):c.624C>T(p.Ala208=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000051 ( 0 hom. )
Consequence
IGLL1
NM_020070.4 synonymous
NM_020070.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.427
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 22-23573284-G-A is Benign according to our data. Variant chr22-23573284-G-A is described in ClinVar as [Benign]. Clinvar id is 2739482.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.427 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGLL1 | NM_020070.4 | c.624C>T | p.Ala208= | synonymous_variant | 3/3 | ENST00000330377.3 | NP_064455.1 | |
IGLL1 | NM_001369906.1 | c.627C>T | p.Ala209= | synonymous_variant | 3/3 | NP_001356835.1 | ||
IGLL1 | NM_152855.3 | c.*253C>T | 3_prime_UTR_variant | 2/2 | NP_690594.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGLL1 | ENST00000330377.3 | c.624C>T | p.Ala208= | synonymous_variant | 3/3 | 1 | NM_020070.4 | ENSP00000329312 | P1 | |
IGLL1 | ENST00000249053.3 | c.*253C>T | 3_prime_UTR_variant | 2/2 | 1 | ENSP00000249053 | ||||
ENST00000458318.2 | n.391-181G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152116Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000262 AC: 66AN: 251438Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135906
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GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 727228
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GnomAD4 genome AF: 0.000151 AC: 23AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74430
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Mar 16, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at