21-46138542-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_206965.2(FTCD):c.1409G>A(p.Arg470Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,586,500 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R470W) has been classified as Uncertain significance.
Frequency
Consequence
NM_206965.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTCD | NM_206965.2 | c.1409G>A | p.Arg470Gln | missense_variant | 12/14 | ENST00000397746.8 | |
FTCD | NM_001320412.2 | c.1409G>A | p.Arg470Gln | missense_variant | 12/15 | ||
FTCD | NM_006657.3 | c.1409G>A | p.Arg470Gln | missense_variant | 12/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTCD | ENST00000397746.8 | c.1409G>A | p.Arg470Gln | missense_variant | 12/14 | 1 | NM_206965.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00128 AC: 194AN: 152136Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00212 AC: 424AN: 199810Hom.: 3 AF XY: 0.00217 AC XY: 240AN XY: 110686
GnomAD4 exome AF: 0.00112 AC: 1613AN: 1434246Hom.: 10 Cov.: 32 AF XY: 0.00120 AC XY: 852AN XY: 712524
GnomAD4 genome ? AF: 0.00128 AC: 195AN: 152254Hom.: 4 Cov.: 33 AF XY: 0.00114 AC XY: 85AN XY: 74432
ClinVar
Submissions by phenotype
Glutamate formiminotransferase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 22, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | FTCD: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at