rs2250656
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000064.4(C3):c.268-111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 1,340,566 control chromosomes in the GnomAD database, including 52,315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5026 hom., cov: 30)
Exomes 𝑓: 0.28 ( 47289 hom. )
Consequence
C3
NM_000064.4 intron
NM_000064.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0330
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 19-6718523-T-C is Benign according to our data. Variant chr19-6718523-T-C is described in ClinVar as [Benign]. Clinvar id is 1276044.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C3 | NM_000064.4 | c.268-111A>G | intron_variant | ENST00000245907.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C3 | ENST00000245907.11 | c.268-111A>G | intron_variant | 1 | NM_000064.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.255 AC: 38684AN: 151744Hom.: 5033 Cov.: 30
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GnomAD4 exome AF: 0.280 AC: 332843AN: 1188704Hom.: 47289 AF XY: 0.278 AC XY: 166140AN XY: 597310
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GnomAD4 genome ? AF: 0.255 AC: 38701AN: 151862Hom.: 5026 Cov.: 30 AF XY: 0.257 AC XY: 19108AN XY: 74212
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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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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at