chr22-37813557-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_014291.4(GCAT):c.524G>T(p.Arg175Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000123 in 1,461,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R175C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014291.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCAT | NM_014291.4 | c.524G>T | p.Arg175Leu | missense_variant | 4/9 | ENST00000248924.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCAT | ENST00000248924.11 | c.524G>T | p.Arg175Leu | missense_variant | 4/9 | 1 | NM_014291.4 | P1 | |
GCAT | ENST00000323205.10 | c.602G>T | p.Arg201Leu | missense_variant | 4/10 | 2 | |||
GCAT | ENST00000451984.1 | c.665G>T | p.Arg222Leu | missense_variant | 4/4 | 3 | |||
GCAT | ENST00000426858.1 | c.*117G>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249566Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135260
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461184Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 726886
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.602G>T (p.R201L) alteration is located in exon 4 (coding exon 4) of the GCAT gene. This alteration results from a G to T substitution at nucleotide position 602, causing the arginine (R) at amino acid position 201 to be replaced by a leucine (L). 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