chr21-33509890-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000819.5(GART):c.2345T>C(p.Ile782Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000766 in 1,613,710 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★).
Frequency
Consequence
NM_000819.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GART | NM_000819.5 | c.2345T>C | p.Ile782Thr | missense_variant | 18/22 | ENST00000381815.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GART | ENST00000381815.9 | c.2345T>C | p.Ile782Thr | missense_variant | 18/22 | 1 | NM_000819.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000414 AC: 63AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000434 AC: 109AN: 251008Hom.: 0 AF XY: 0.000398 AC XY: 54AN XY: 135672
GnomAD4 exome AF: 0.000803 AC: 1173AN: 1461422Hom.: 1 Cov.: 31 AF XY: 0.000741 AC XY: 539AN XY: 727018
GnomAD4 genome ? AF: 0.000414 AC: 63AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000389 AC XY: 29AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.2345T>C (p.I782T) alteration is located in exon 18 (coding exon 17) of the GART gene. This alteration results from a T to C substitution at nucleotide position 2345, causing the isoleucine (I) at amino acid position 782 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at