chr9-134885254-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004108.3(FCN2):c.317A>G(p.Lys106Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000892 in 1,614,052 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00085 ( 16 hom. )
Consequence
FCN2
NM_004108.3 missense
NM_004108.3 missense
Scores
1
18
Clinical Significance
Conservation
PhyloP100: 1.04
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.006575167).
BP6
?
Variant 9-134885254-A-G is Benign according to our data. Variant chr9-134885254-A-G is described in ClinVar as [Benign]. Clinvar id is 2659703.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCN2 | NM_004108.3 | c.317A>G | p.Lys106Arg | missense_variant | 5/8 | ENST00000291744.11 | |
FCN2 | NM_015837.3 | c.203A>G | p.Lys68Arg | missense_variant | 4/7 | ||
FCN2 | XM_011518392.4 | c.284A>G | p.Lys95Arg | missense_variant | 5/8 | ||
FCN2 | XM_006717015.5 | c.170A>G | p.Lys57Arg | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCN2 | ENST00000291744.11 | c.317A>G | p.Lys106Arg | missense_variant | 5/8 | 1 | NM_004108.3 | P1 | |
FCN2 | ENST00000350339.3 | c.203A>G | p.Lys68Arg | missense_variant | 4/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00128 AC: 195AN: 152128Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00130 AC: 326AN: 251252Hom.: 2 AF XY: 0.00115 AC XY: 156AN XY: 135838
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GnomAD4 exome AF: 0.000853 AC: 1247AN: 1461806Hom.: 16 Cov.: 32 AF XY: 0.000876 AC XY: 637AN XY: 727222
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GnomAD4 genome ? AF: 0.00127 AC: 193AN: 152246Hom.: 1 Cov.: 33 AF XY: 0.00121 AC XY: 90AN XY: 74446
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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 | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | FCN2: BP4, BS1, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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