chr1-22659292-AGATG-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001378156.1(C1QB):c.-23-115_-23-112del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 646,424 control chromosomes in the GnomAD database, including 3,520 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.084 ( 468 hom., cov: 0)
Exomes 𝑓: 0.093 ( 3052 hom. )
Consequence
C1QB
NM_001378156.1 intron
NM_001378156.1 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.22
Genes affected
C1QB (HGNC:1242): (complement C1q B chain) This gene encodes the B-chain polypeptide of serum complement subcomponent C1q, which associates with C1r and C1s to yield the first component of the serum complement system. C1q is composed of 18 polypeptide chains which include 6 A-chains, 6 B-chains, and 6 C-chains. Each chain contains an N-terminal collagen-like region and a C-terminal C1q globular domain. C1q deficiency is associated with lupus erythematosus and glomerulonephritis. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 1-22659292-AGATG-A is Benign according to our data. Variant chr1-22659292-AGATG-A is described in ClinVar as [Benign]. Clinvar id is 1252299.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1QB | NM_001378156.1 | c.-23-115_-23-112del | intron_variant | ENST00000509305.6 | |||
C1QB | NM_000491.5 | c.-17-115_-17-112del | intron_variant | ||||
C1QB | NM_001371184.3 | c.-23-115_-23-112del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QB | ENST00000509305.6 | c.-23-115_-23-112del | intron_variant | 1 | NM_001378156.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0838 AC: 10785AN: 128634Hom.: 467 Cov.: 0
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GnomAD4 exome AF: 0.0928 AC: 48060AN: 517656Hom.: 3052 AF XY: 0.0978 AC XY: 26681AN XY: 272788
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GnomAD4 genome ? AF: 0.0840 AC: 10811AN: 128768Hom.: 468 Cov.: 0 AF XY: 0.0827 AC XY: 5101AN XY: 61688
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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 | GeneDx | Jun 18, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at