9-76502424-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001490.5(GCNT1):āc.43A>Cā(p.Thr15Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,226 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 (ā ).
Frequency
Consequence
NM_001490.5 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 |
---|---|---|---|---|---|---|---|
GCNT1 | NM_001490.5 | c.43A>C | p.Thr15Pro | missense_variant | 4/4 | ENST00000376730.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCNT1 | ENST00000376730.5 | c.43A>C | p.Thr15Pro | missense_variant | 4/4 | 1 | NM_001490.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151972Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250988Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135690
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461254Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726956
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151972Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.43A>C (p.T15P) alteration is located in exon 3 (coding exon 1) of the GCNT1 gene. This alteration results from a A to C substitution at nucleotide position 43, causing the threonine (T) at amino acid position 15 to be replaced by a proline (P). 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