chr9-135626177-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182974.3(GLT6D1):c.149A>G(p.Asp50Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182974.3 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 |
---|---|---|---|---|---|---|---|
GLT6D1 | NM_182974.3 | c.149A>G | p.Asp50Gly | missense_variant | 4/5 | ENST00000371763.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT6D1 | ENST00000371763.6 | c.149A>G | p.Asp50Gly | missense_variant | 4/5 | 1 | NM_182974.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152050Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249466Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135334
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461684Hom.: 0 Cov.: 35 AF XY: 0.00000550 AC XY: 4AN XY: 727134
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152050Hom.: 0 Cov.: 34 AF XY: 0.0000539 AC XY: 4AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.149A>G (p.D50G) alteration is located in exon 4 (coding exon 3) of the GLT6D1 gene. This alteration results from a A to G substitution at nucleotide position 149, causing the aspartic acid (D) at amino acid position 50 to be replaced by a glycine (G). 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