1-22647255-ACC-AC
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_172369.5(C1QC):βc.213delβ(p.Gln74ArgfsTer64) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 1,608,950 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β ). Synonymous variant affecting the same amino acid position (i.e. P71P) has been classified as Benign.
Frequency
Consequence
NM_172369.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1QC | NM_172369.5 | c.213del | p.Gln74ArgfsTer64 | frameshift_variant | 3/3 | ENST00000374640.9 | |
C1QC | NM_001114101.3 | c.213del | p.Gln74ArgfsTer64 | frameshift_variant | 3/3 | ||
C1QC | NM_001347619.2 | c.213del | p.Gln74ArgfsTer64 | frameshift_variant | 3/3 | ||
C1QC | NM_001347620.2 | c.-55del | 5_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QC | ENST00000374640.9 | c.213del | p.Gln74ArgfsTer64 | frameshift_variant | 3/3 | 1 | NM_172369.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151902Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000817 AC: 2AN: 244682Hom.: 0 AF XY: 0.00000752 AC XY: 1AN XY: 133012
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1457048Hom.: 0 Cov.: 32 AF XY: 0.0000221 AC XY: 16AN XY: 725020
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151902Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74176
ClinVar
Submissions by phenotype
C1Q deficiency 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 1996 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 28, 2022 | This sequence change creates a premature translational stop signal (p.Gln74Argfs*64) in the C1QC gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 172 amino acid(s) of the C1QC protein. This variant is present in population databases (rs761681612, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with systemic lupus erythematosus (PMID: 8630118). This variant is also known as deletion C at codon 43. ClinVar contains an entry for this variant (Variation ID: 17069). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at