chr12-128876053-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144669.3(GLT1D1):c.208C>T(p.Leu70Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,603,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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
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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.208C>T | p.Leu70Phe | missense_variant | 2/12 | ENST00000442111.7 | |
GLT1D1 | NR_159493.1 | n.312C>T | non_coding_transcript_exon_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT1D1 | ENST00000442111.7 | c.208C>T | p.Leu70Phe | missense_variant | 2/12 | 5 | NM_001366886.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000208 AC: 5AN: 240334Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 129892
GnomAD4 exome AF: 0.0000200 AC: 29AN: 1451114Hom.: 0 Cov.: 31 AF XY: 0.0000222 AC XY: 16AN XY: 721392
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2023 | The c.208C>T (p.L70F) alteration is located in exon 2 (coding exon 2) of the GLT1D1 gene. This alteration results from a C to T substitution at nucleotide position 208, causing the leucine (L) at amino acid position 70 to be replaced by a phenylalanine (F). 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