rs1071583
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002003.5(FCN1):āc.825A>Gā(p.Gln275=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 1,613,890 control chromosomes in the GnomAD database, including 339,132 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: š 0.70 ( 38568 hom., cov: 32)
Exomes š: 0.64 ( 300564 hom. )
Consequence
FCN1
NM_002003.5 synonymous
NM_002003.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.41
Genes affected
FCN1 (HGNC:3623): (ficolin 1) The ficolin family of proteins are characterized by the presence of a leader peptide, a short N-terminal segment, followed by a collagen-like region, and a C-terminal fibrinogen-like domain. The collagen-like and the fibrinogen-like domains are also found separately in other proteins such as complement protein C1q, C-type lectins known as collectins, and tenascins. However, all these proteins recognize different targets, and are functionally distinct. Ficolin 1 encoded by FCN1 is predominantly expressed in the peripheral blood leukocytes, and has been postulated to function as a plasma protein with elastin-binding activity. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP7
?
Synonymous conserved (PhyloP=-3.41 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCN1 | NM_002003.5 | c.825A>G | p.Gln275= | synonymous_variant | 9/9 | ENST00000371806.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCN1 | ENST00000371806.4 | c.825A>G | p.Gln275= | synonymous_variant | 9/9 | 1 | NM_002003.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.699 AC: 106287AN: 151982Hom.: 38522 Cov.: 32
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GnomAD3 exomes AF: 0.625 AC: 157129AN: 251484Hom.: 51247 AF XY: 0.633 AC XY: 86036AN XY: 135916
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GnomAD4 exome AF: 0.637 AC: 931227AN: 1461790Hom.: 300564 Cov.: 48 AF XY: 0.640 AC XY: 465480AN XY: 727208
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GnomAD4 genome ? AF: 0.699 AC: 106380AN: 152100Hom.: 38568 Cov.: 32 AF XY: 0.697 AC XY: 51829AN XY: 74336
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at