9-134887245-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_004108.3(FCN2):c.772G>T(p.Ala258Ser) variant causes a missense change. The variant allele was found at a frequency of 0.117 in 1,614,000 control chromosomes in the GnomAD database, including 11,750 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_004108.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FCN2 | NM_004108.3 | c.772G>T | p.Ala258Ser | missense_variant | Exon 8 of 8 | ENST00000291744.11 | NP_004099.2 | |
FCN2 | NM_015837.3 | c.658G>T | p.Ala220Ser | missense_variant | Exon 7 of 7 | NP_056652.1 | ||
FCN2 | XM_011518392.4 | c.739G>T | p.Ala247Ser | missense_variant | Exon 8 of 8 | XP_011516694.1 | ||
FCN2 | XM_006717015.5 | c.625G>T | p.Ala209Ser | missense_variant | Exon 7 of 7 | XP_006717078.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.135 AC: 20474AN: 152124Hom.: 1456 Cov.: 33
GnomAD3 exomes AF: 0.125 AC: 31345AN: 251484Hom.: 2226 AF XY: 0.123 AC XY: 16655AN XY: 135916
GnomAD4 exome AF: 0.115 AC: 168439AN: 1461758Hom.: 10294 Cov.: 36 AF XY: 0.115 AC XY: 83401AN XY: 727180
GnomAD4 genome AF: 0.135 AC: 20497AN: 152242Hom.: 1456 Cov.: 33 AF XY: 0.133 AC XY: 9896AN XY: 74438
ClinVar
Submissions by phenotype
FCN2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at