rs200679529
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_000156.6(GAMT):c.600C>T(p.Ala200Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,607,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000156.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAMT | ENST00000252288.8 | c.600C>T | p.Ala200Ala | synonymous_variant | Exon 6 of 6 | 1 | NM_000156.6 | ENSP00000252288.1 | ||
GAMT | ENST00000640762.1 | c.531C>T | p.Ala177Ala | synonymous_variant | Exon 6 of 6 | 5 | ENSP00000492031.1 | |||
GAMT | ENST00000640164.1 | n.433C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245250Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133414
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1455616Hom.: 0 Cov.: 31 AF XY: 0.00000966 AC XY: 7AN XY: 724338
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
GAMT: BP4, BP7 -
Cerebral creatine deficiency syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at