9-134885254-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004108.3(FCN2):āc.317A>Gā(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 (ā ).
Frequency
Consequence
NM_004108.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FCN2 | NM_004108.3 | c.317A>G | p.Lys106Arg | missense_variant | 5/8 | ENST00000291744.11 | NP_004099.2 | |
FCN2 | NM_015837.3 | c.203A>G | p.Lys68Arg | missense_variant | 4/7 | NP_056652.1 | ||
FCN2 | XM_011518392.4 | c.284A>G | p.Lys95Arg | missense_variant | 5/8 | XP_011516694.1 | ||
FCN2 | XM_006717015.5 | c.170A>G | p.Lys57Arg | missense_variant | 4/7 | XP_006717078.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FCN2 | ENST00000291744.11 | c.317A>G | p.Lys106Arg | missense_variant | 5/8 | 1 | NM_004108.3 | ENSP00000291744.6 | ||
FCN2 | ENST00000350339.3 | c.203A>G | p.Lys68Arg | missense_variant | 4/7 | 5 | ENSP00000291741.5 |
Frequencies
GnomAD3 genomes AF: 0.00128 AC: 195AN: 152128Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00130 AC: 326AN: 251252Hom.: 2 AF XY: 0.00115 AC XY: 156AN XY: 135838
GnomAD4 exome AF: 0.000853 AC: 1247AN: 1461806Hom.: 16 Cov.: 32 AF XY: 0.000876 AC XY: 637AN XY: 727222
GnomAD4 genome AF: 0.00127 AC: 193AN: 152246Hom.: 1 Cov.: 33 AF XY: 0.00121 AC XY: 90AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | FCN2: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at