1-22644037-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_172369.5(C1QC):āc.14C>Gā(p.Pro5Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000348 in 1,437,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_172369.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1QC | NM_172369.5 | c.14C>G | p.Pro5Arg | missense_variant | 2/3 | ENST00000374640.9 | NP_758957.2 | |
C1QC | NM_001114101.3 | c.14C>G | p.Pro5Arg | missense_variant | 2/3 | NP_001107573.1 | ||
C1QC | NM_001347619.2 | c.14C>G | p.Pro5Arg | missense_variant | 2/3 | NP_001334548.1 | ||
C1QC | NM_001347620.2 | c.-87+323C>G | intron_variant | NP_001334549.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1QC | ENST00000374640.9 | c.14C>G | p.Pro5Arg | missense_variant | 2/3 | 1 | NM_172369.5 | ENSP00000363771 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000484 AC: 1AN: 206406Hom.: 0 AF XY: 0.00000902 AC XY: 1AN XY: 110836
GnomAD4 exome AF: 0.00000348 AC: 5AN: 1437526Hom.: 0 Cov.: 31 AF XY: 0.00000421 AC XY: 3AN XY: 712356
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 25, 2022 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with C1QC-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.004%). This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 5 of the C1QC protein (p.Pro5Arg). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at