9-76502472-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001490.5(GCNT1):c.91G>A(p.Val31Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,613,448 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 (★).
Frequency
Consequence
NM_001490.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GCNT1 | NM_001490.5 | c.91G>A | p.Val31Ile | missense_variant | 4/4 | ENST00000376730.5 | NP_001481.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GCNT1 | ENST00000376730.5 | c.91G>A | p.Val31Ile | missense_variant | 4/4 | 1 | NM_001490.5 | ENSP00000365920.4 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152036Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251370Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135870
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461412Hom.: 0 Cov.: 30 AF XY: 0.0000426 AC XY: 31AN XY: 727018
GnomAD4 genome AF: 0.0000724 AC: 11AN: 152036Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2024 | The c.91G>A (p.V31I) alteration is located in exon 3 (coding exon 1) of the GCNT1 gene. This alteration results from a G to A substitution at nucleotide position 91, causing the valine (V) at amino acid position 31 to be replaced by an isoleucine (I). 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