9-133154205-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_021996.6(GBGT1):c.416G>A(p.Gly139Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000282 in 1,557,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021996.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBGT1 | ENST00000372040.9 | c.416G>A | p.Gly139Glu | missense_variant | Exon 7 of 7 | 1 | NM_021996.6 | ENSP00000361110.3 | ||
ENSG00000285245 | ENST00000647146.1 | c.396+973G>A | intron_variant | Intron 6 of 22 | ENSP00000493691.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 6AN: 213962Hom.: 0 AF XY: 0.0000523 AC XY: 6AN XY: 114814
GnomAD4 exome AF: 0.0000270 AC: 38AN: 1405632Hom.: 0 Cov.: 31 AF XY: 0.0000231 AC XY: 16AN XY: 691390
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.416G>A (p.G139E) alteration is located in exon 7 (coding exon 6) of the GBGT1 gene. This alteration results from a G to A substitution at nucleotide position 416, causing the glycine (G) at amino acid position 139 to be replaced by a glutamic acid (E). 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