rs344550
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000064.4(C3):c.4173-713G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 154,050 control chromosomes in the GnomAD database, including 32,037 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.64 ( 31693 hom., cov: 32)
Exomes 𝑓: 0.58 ( 344 hom. )
Consequence
C3
NM_000064.4 intron
NM_000064.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.457
Genes affected
C3 (HGNC:1318): (complement C3) Complement component C3 plays a central role in the activation of complement system. Its activation is required for both classical and alternative complement activation pathways. The encoded preproprotein is proteolytically processed to generate alpha and beta subunits that form the mature protein, which is then further processed to generate numerous peptide products. The C3a peptide, also known as the C3a anaphylatoxin, modulates inflammation and possesses antimicrobial activity. Mutations in this gene are associated with atypical hemolytic uremic syndrome and age-related macular degeneration in human patients. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C3 | NM_000064.4 | c.4173-713G>C | intron_variant | ENST00000245907.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C3 | ENST00000245907.11 | c.4173-713G>C | intron_variant | 1 | NM_000064.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.644 AC: 97948AN: 151980Hom.: 31672 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.581 AC: 1135AN: 1952Hom.: 344 Cov.: 0 AF XY: 0.574 AC XY: 561AN XY: 978
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GnomAD4 genome ? AF: 0.644 AC: 98019AN: 152098Hom.: 31693 Cov.: 32 AF XY: 0.643 AC XY: 47820AN XY: 74346
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at