chr21-46136999-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000397748.5(FTCD):c.1594C>T(p.Pro532Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,613,416 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 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. P532L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000397748.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTCD | NM_206965.2 | c.1614C>T | p.Thr538= | synonymous_variant | 14/14 | ENST00000397746.8 | |
FTCD | NM_001320412.2 | c.1594C>T | p.Pro532Ser | missense_variant | 14/15 | ||
FTCD | NM_006657.3 | c.1614C>T | p.Thr538= | synonymous_variant | 14/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTCD | ENST00000397746.8 | c.1614C>T | p.Thr538= | synonymous_variant | 14/14 | 1 | NM_206965.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000133 AC: 33AN: 247832Hom.: 1 AF XY: 0.000119 AC XY: 16AN XY: 134594
GnomAD4 exome AF: 0.000138 AC: 201AN: 1461082Hom.: 1 Cov.: 36 AF XY: 0.000131 AC XY: 95AN XY: 726812
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74486
ClinVar
Submissions by phenotype
Glutamate formiminotransferase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at