chr12-128957599-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144669.3(GLT1D1):c.595G>C(p.Val199Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign 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. V199M) has been classified as Uncertain significance.
Frequency
Consequence
NM_144669.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLT1D1 | NM_001366886.1 | c.835G>C | p.Val279Leu | missense_variant | 11/12 | ENST00000442111.7 | |
GLT1D1 | NR_159493.1 | n.845G>C | non_coding_transcript_exon_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT1D1 | ENST00000442111.7 | c.835G>C | p.Val279Leu | missense_variant | 11/12 | 5 | NM_001366886.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251432Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135900
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461568Hom.: 0 Cov.: 29 AF XY: 0.0000454 AC XY: 33AN XY: 727110
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2023 | The c.595G>C (p.V199L) alteration is located in exon 7 (coding exon 7) of the GLT1D1 gene. This alteration results from a G to C substitution at nucleotide position 595, causing the valine (V) at amino acid position 199 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