chr2-157258437-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014568.3(GALNT5):c.355G>C(p.Gly119Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000932 in 1,608,896 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_014568.3 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 |
---|---|---|---|---|---|---|---|
GALNT5 | NM_014568.3 | c.355G>C | p.Gly119Arg | missense_variant | 1/10 | ENST00000259056.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT5 | ENST00000259056.5 | c.355G>C | p.Gly119Arg | missense_variant | 1/10 | 1 | NM_014568.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151144Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000409 AC: 1AN: 244732Hom.: 0 AF XY: 0.00000755 AC XY: 1AN XY: 132478
GnomAD4 exome AF: 0.00000823 AC: 12AN: 1457752Hom.: 0 Cov.: 33 AF XY: 0.00000690 AC XY: 5AN XY: 725078
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151144Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73768
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2021 | The c.355G>C (p.G119R) alteration is located in exon 1 (coding exon 1) of the GALNT5 gene. This alteration results from a G to C substitution at nucleotide position 355, causing the glycine (G) at amino acid position 119 to be replaced by an arginine (R). 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