rs34789496
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_004108.3(FCN2):c.543C>T(p.His181=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 1,613,114 control chromosomes in the GnomAD database, including 1,110 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 0.019 ( 165 hom., cov: 32)
Exomes 𝑓: 0.011 ( 945 hom. )
Consequence
FCN2
NM_004108.3 synonymous
NM_004108.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.19
Genes affected
FCN2 (HGNC:3624): (ficolin 2) The product of this gene belongs to the ficolin family of proteins. This family is 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. This gene is predominantly expressed in the liver, and has been shown to have carbohydrate binding and opsonic activities. Alternatively spliced transcript variants encoding different isoforms have been identified. [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=-0.78).
BP7
?
Synonymous conserved (PhyloP=-2.19 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCN2 | NM_004108.3 | c.543C>T | p.His181= | synonymous_variant | 6/8 | ENST00000291744.11 | |
FCN2 | NM_015837.3 | c.429C>T | p.His143= | synonymous_variant | 5/7 | ||
FCN2 | XM_011518392.4 | c.510C>T | p.His170= | synonymous_variant | 6/8 | ||
FCN2 | XM_006717015.5 | c.396C>T | p.His132= | synonymous_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCN2 | ENST00000291744.11 | c.543C>T | p.His181= | synonymous_variant | 6/8 | 1 | NM_004108.3 | P1 | |
FCN2 | ENST00000350339.3 | c.429C>T | p.His143= | synonymous_variant | 5/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0194 AC: 2948AN: 151922Hom.: 160 Cov.: 32
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GnomAD3 exomes AF: 0.0304 AC: 7586AN: 249476Hom.: 439 AF XY: 0.0257 AC XY: 3474AN XY: 134988
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GnomAD4 exome AF: 0.0106 AC: 15528AN: 1461074Hom.: 945 Cov.: 32 AF XY: 0.0102 AC XY: 7380AN XY: 726834
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GnomAD4 genome ? AF: 0.0195 AC: 2962AN: 152040Hom.: 165 Cov.: 32 AF XY: 0.0232 AC XY: 1720AN XY: 74296
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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