chr6-32029581-G-GCT
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001002029.4(C4B):c.3694_3695dup(p.Val1233GlnfsTer75) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0042 ( 0 hom., cov: 26)
Exomes 𝑓: 0.0077 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
C4B
NM_001002029.4 frameshift
NM_001002029.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.53
Genes affected
C4B (HGNC:1324): (complement C4B (Chido/Rodgers blood group)) This gene encodes the basic form of complement factor 4, and together with the C4A gene, is part of the classical activation pathway. The protein is expressed as a single chain precursor which is proteolytically cleaved into a trimer of alpha, beta, and gamma chains prior to secretion. The trimer provides a surface for interaction between the antigen-antibody complex and other complement components. The alpha chain may be cleaved to release C4 anaphylatoxin, a mediator of local inflammation. Deficiency of this protein is associated with systemic lupus erythematosus. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. Varying haplotypes of this gene cluster exist, such that individuals may have 1, 2, or 3 copies of this gene. In addition, this gene exists as a long form and a short form due to the presence or absence of a 6.4 kb endogenous HERV-K retrovirus in intron 9. [provided by RefSeq, May 2020]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 6-32029581-G-GCT is Benign according to our data. Variant chr6-32029581-G-GCT is described in ClinVar as [Benign]. Clinvar id is 2656436.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C4B | NM_001002029.4 | c.3694_3695dup | p.Val1233GlnfsTer75 | frameshift_variant | 29/41 | ENST00000435363.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4B | ENST00000435363.7 | c.3694_3695dup | p.Val1233GlnfsTer75 | frameshift_variant | 29/41 | 1 | NM_001002029.4 | P1 | |
C4B | ENST00000425700.3 | c.3694_3695dup | p.Val1233GlnfsTer75 | frameshift_variant | 29/40 | 1 | |||
C4B | ENST00000647698.1 | c.2400_2401dup | p.Val802GlnfsTer75 | frameshift_variant | 19/31 | ||||
C4B | ENST00000648821.1 | n.2307_2308dup | non_coding_transcript_exon_variant | 16/27 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 617AN: 146762Hom.: 0 Cov.: 26 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00769 AC: 11017AN: 1433524Hom.: 0 Cov.: 34 AF XY: 0.00737 AC XY: 5256AN XY: 713360
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00420 AC: 617AN: 146882Hom.: 0 Cov.: 26 AF XY: 0.00446 AC XY: 319AN XY: 71558
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | C4B: BS1, BS2 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at