12-103996847-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001384711.1(GLT8D2):c.488G>A(p.Gly163Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000622 in 1,608,266 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001384711.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLT8D2 | NM_001384711.1 | c.488G>A | p.Gly163Asp | missense_variant, splice_region_variant | Exon 8 of 11 | ENST00000360814.9 | NP_001371640.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLT8D2 | ENST00000360814.9 | c.488G>A | p.Gly163Asp | missense_variant, splice_region_variant | Exon 8 of 11 | 1 | NM_001384711.1 | ENSP00000354053.4 | ||
GLT8D2 | ENST00000546436.5 | c.488G>A | p.Gly163Asp | missense_variant, splice_region_variant | Exon 7 of 10 | 5 | ENSP00000449750.1 | |||
GLT8D2 | ENST00000548660.5 | c.488G>A | p.Gly163Asp | missense_variant, splice_region_variant | Exon 8 of 11 | 2 | ENSP00000447450.1 | |||
GLT8D2 | ENST00000552572.1 | n.-1G>A | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247778Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133914
GnomAD4 exome AF: 0.00000618 AC: 9AN: 1456066Hom.: 0 Cov.: 28 AF XY: 0.00000414 AC XY: 3AN XY: 724556
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.488G>A (p.G163D) alteration is located in exon 8 (coding exon 6) of the GLT8D2 gene. This alteration results from a G to A substitution at nucleotide position 488, causing the glycine (G) at amino acid position 163 to be replaced by an aspartic acid (D). 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