chr21-46136482-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000397748.5(FTCD):c.1691C>A(p.Thr564Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000938 in 1,612,630 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000397748.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTCD | NM_001320412.2 | c.1691C>A | p.Thr564Lys | missense_variant | 15/15 | ||
FTCD | NM_006657.3 | c.*15C>A | 3_prime_UTR_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTCD | ENST00000397748.5 | c.1691C>A | p.Thr564Lys | missense_variant | 15/15 | 1 | |||
FTCD | ENST00000291670.9 | c.*15C>A | 3_prime_UTR_variant | 15/15 | 1 | P1 | |||
FTCD | ENST00000460011.6 | c.*85C>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00425 AC: 647AN: 152118Hom.: 3 Cov.: 30
GnomAD3 exomes AF: 0.00124 AC: 300AN: 242800Hom.: 2 AF XY: 0.000996 AC XY: 133AN XY: 133472
GnomAD4 exome AF: 0.000592 AC: 865AN: 1460394Hom.: 6 Cov.: 31 AF XY: 0.000519 AC XY: 377AN XY: 726472
GnomAD4 genome ? AF: 0.00425 AC: 647AN: 152236Hom.: 3 Cov.: 30 AF XY: 0.00402 AC XY: 299AN XY: 74444
ClinVar
Submissions by phenotype
Glutamate formiminotransferase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Myosclerosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
FTCD-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 08, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Collagen 6-related myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at