12-128899280-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144669.3(GLT1D1):c.368C>T(p.Ala123Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000732 in 1,613,106 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_144669.3 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 |
---|---|---|---|---|---|---|---|
GLT1D1 | NM_001366886.1 | c.368C>T | p.Ala123Val | missense_variant | 4/12 | ENST00000442111.7 | |
GLT1D1 | NR_159493.1 | n.472C>T | non_coding_transcript_exon_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT1D1 | ENST00000442111.7 | c.368C>T | p.Ala123Val | missense_variant | 4/12 | 5 | NM_001366886.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000178 AC: 27AN: 152066Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251460Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135902
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1460922Hom.: 0 Cov.: 29 AF XY: 0.0000660 AC XY: 48AN XY: 726830
GnomAD4 genome AF: 0.000177 AC: 27AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.368C>T (p.A123V) alteration is located in exon 4 (coding exon 4) of the GLT1D1 gene. This alteration results from a C to T substitution at nucleotide position 368, causing the alanine (A) at amino acid position 123 to be replaced by a valine (V). 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